AIP & Foods

AIP Glossary

Plain-language definitions of the terms used across the food lists, recipes, and articles. Education, not medical advice.

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25-hydroxy vitamin D

This is the form of vitamin D measured in a standard blood test to check vitamin D status. It reflects what is stored in the body rather than what is circulating in its active hormone form. Low levels are common in autoimmune disease and are worth tracking over time.

Reference: Consensus Statement on Vitamin D Status Assessment and Supplementation: Whys, Whens, and Hows. (Endocrine reviews, 2024) via PubMed

Acai

Acai is a small dark purple berry that grows on a palm tree in the Amazon, usually sold frozen as pulp or dried into powder. It is a concentrated source of anthocyanin antioxidants. On the Autoimmune Protocol it is used the same way as other berries, in moderation.

See also: On the food list

Acerola

Acerola is a small, tart red fruit that looks like a cherry and grows in tropical climates. It carries an unusually high amount of vitamin C for its size, which is why it shows up in whole-food vitamin C powders. A few acerola cherries can meet a full day's vitamin C need.

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Acorn squash

Acorn squash is a small winter squash with ridged dark green skin and sweet, dense orange flesh. It roasts well cut in half and filled with something savory. It is a good source of fiber and carotenoids and fits easily into Autoimmune Protocol meals.

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Adaptive immunity

Adaptive immunity is the part of the immune system that learns. It builds a targeted response to a specific threat using T cells and B cells, then remembers that threat for a faster reaction later. In autoimmune disease this is the system misdirected at the body's own tissue.

Reference: Principles and therapeutic applications of adaptive immunity. (Cell, 2024) via PubMed

Adaptogens

Adaptogens are a category of herbs, including ashwagandha, rhodiola, and holy basil, traditionally used to help the body handle stress. The idea is that they support a more balanced stress response rather than pushing the body in one direction. Not every adaptogen suits every autoimmune condition, so individual response matters.

Adobo

Adobo refers to both a seasoning blend and a cooking method from Filipino and Latin American kitchens, built on vinegar, garlic, and spices simmered with meat or vegetables. The vinegar and long simmer create a tangy, savory dish. On the Autoimmune Protocol it is easy to adapt by leaving out any nightshade spices.

Adrenal dysfunction

Adrenal dysfunction describes a pattern where cortisol release becomes out of sync with the body's actual needs, often from prolonged stress. It differs from adrenal failure, a distinct medical diagnosis. This pattern matters in autoimmune healing because chronic stress signaling keeps the immune system on alert.

Reference: Chronic Stress and Autoimmunity: The Role of HPA Axis and Cortisol Dysregulation. (International journal of molecular sciences, 2025) via PubMed

Adrenal glands

The adrenal glands are two small glands that sit above each kidney. They produce cortisol, adrenaline, aldosterone, and a portion of the body's androgens, hormones that govern the stress response, blood pressure, and metabolism. Their output shifts constantly with daily rhythm and stress load.

Adrenaline (epinephrine)

Adrenaline, also called epinephrine, is a fast-acting hormone released by the adrenal glands in moments of stress or threat. It raises heart rate, sharpens focus, and pushes stored energy into the bloodstream for quick use. It is meant to switch off once the stressor passes.

AIP (Autoimmune Protocol)

The Autoimmune Protocol, or AIP, is a structured way of eating that removes foods known to commonly aggravate the gut lining or immune system, then reintroduces them one at a time. The removal phase is temporary. The goal is to learn which foods a person's body tolerates and which keep symptoms active.

Reference: Autoimmune protocol diet: A personalized elimination diet for patients with autoimmune diseases. (Metabolism open, 2024) via PubMed

Aldosterone

Aldosterone is a hormone made by the adrenal glands that helps the kidneys regulate the balance of sodium and potassium in the body. That balance directly affects blood pressure and fluid levels. It works alongside cortisol as part of the broader adrenal hormone picture.

Alopecia areata

Alopecia areata is an autoimmune condition in which the immune system attacks hair follicles, causing patches of hair loss on the scalp or body. It can come and go unpredictably and is not caused by anything a person did wrong. Like other autoimmune conditions, it involves a mix of genetic and environmental triggers.

Reference: Alopecia areata. (Nature reviews. Disease primers, 2017) via PubMed

Amaranth leaves

Amaranth leaves are the tender leaves of the amaranth plant, a relative of spinach and chard, known in different cuisines as callaloo, chaulai, or een choy. They cook down quickly and work in the same dishes spinach would. They provide iron, calcium, and other minerals.

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Ambarella

Ambarella, also called June plum or amra, is a tropical fruit with crisp, tart flesh when firm and a softer, sweeter texture as it ripens. It is eaten out of hand, added to salads, or cooked into chutneys. It provides vitamin C along with fiber.

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Amchur

Amchur, also spelled amchoor, is a tart spice made from dried, ground unripe mangoes, used across Indian cooking to add sourness without liquid. A small amount goes into curries, chutneys, and spice blends. It gives dishes a bright, tangy edge instead of vinegar or citrus.

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Androgens

Androgens are a group of hormones, including testosterone and DHEA, produced by the ovaries, testes, and adrenal glands. Every body makes some androgens, just in different amounts. They influence muscle, bone, energy, and libido, and their balance can shift with adrenal or ovarian function.

Anemia

Anemia is a state of having too few healthy red blood cells or too little hemoglobin, which lowers the blood's capacity to carry oxygen. Low iron, low B12, or low folate are common causes and can also happen alongside gut inflammation that limits absorption. It is worth ruling out as a contributor to fatigue in autoimmune disease.

Reference: Anemia of inflammation. (Blood, 2018) via PubMed

Ankylosing spondylitis

Ankylosing spondylitis is a form of inflammatory arthritis that primarily affects the spine and the joints connecting the spine to the pelvis, causing stiffness and pain that is often worse in the morning. Over time it can affect posture and mobility if untreated. It shares genetic and immune features with other autoimmune-related conditions.

Reference: Ankylosing spondylitis: an autoimmune or autoinflammatory disease? (Nature reviews. Rheumatology, 2021) via PubMed

Annatto

Annatto is a natural coloring and mild seasoning made from the seeds of the achiote tree, giving foods a warm orange-red hue without dye. It is common in Latin American and Caribbean cooking and in some dairy products. It carries a subtly earthy, slightly peppery flavor.

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Anovulatory cycle

An anovulatory cycle is a menstrual cycle in which the ovary does not release an egg, so progesterone stays low that month. Without enough progesterone to balance it, estrogen can end up relatively unopposed. This becomes more common with age, stress, and thyroid or adrenal imbalance.

Anthocyanin

Anthocyanin is the purple-blue pigment that gives berries, purple cabbage, and other deep-colored produce their color. It belongs to a class of plant compounds studied for antioxidant activity. Eating a range of colorful produce is one simple way to bring in a variety of these compounds.

Antibody

An antibody is a protein the immune system builds to tag a specific target, whether a virus, bacteria, or, in autoimmune disease, the body's own tissue. In autoimmune thyroid disease, for example, antibodies like anti-TPO are aimed at the thyroid itself. Antibody levels are often tracked over time as a marker of immune activity.

Reference: Thyroid autoantibodies. (Journal of clinical pathology, 2022) via PubMed

Antigen

An antigen is anything the immune system can recognize and respond to, such as a protein from a virus, a food particle, or the body's own tissue. Recognizing an antigen is what triggers an immune response. In autoimmune disease, the antigen being targeted belongs to the body itself.

Antinuclear antibody (ANA)

The antinuclear antibody test, or ANA, checks the blood for antibodies directed at the nucleus of the body's own cells. It is often used as a first screening step when autoimmune disease is suspected. A positive ANA alone does not confirm a diagnosis, since it can appear in healthy people too.

Reference: Understanding and interpreting antinuclear antibody tests in systemic rheumatic diseases. (Nature reviews. Rheumatology, 2020) via PubMed

Antioxidant

An antioxidant is a substance that neutralizes free radicals, unstable molecules that can damage cells when they build up faster than the body can clear them. Antioxidants come from a wide range of colorful fruits and vegetables as well as the body's own internal defenses. Variety in the diet is more useful than any single high-antioxidant food.

Arame

Arame is a mild-tasting sea vegetable that grows in thin, dark strands and is sold dried. It is soaked briefly before going into salads, soups, or stir-fries. Like other sea vegetables it provides iodine and trace minerals, worth being mindful of for anyone managing thyroid dosing.

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Aril

An aril is the fleshy covering that surrounds certain seeds. Mace, the spice, is the aril of the nutmeg seed, and the juicy red seeds eaten from a pomegranate are technically arils rather than true seeds. It is a botanical term that shows up occasionally in ingredient lists.

Aromatase

Aromatase is an enzyme that converts testosterone into estrogen in fat tissue, the ovaries, and other sites throughout the body. Its activity tends to rise with more body fat and with inflammation. Because it shifts hormone balance toward more estrogen, aromatase activity is one piece of the picture in hormone-related autoimmune conditions.

Reference: Estrogen: The necessary evil for human health, and ways to tame it. (Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 2018) via PubMed

Arrowroot

Arrowroot is a fine white starch ground from the root of the arrowroot plant, used to thicken sauces, soups, and gravies without the grittiness some starches leave behind. In Autoimmune Protocol baking it stands in for grain flours and helps create a lighter texture. It has little flavor of its own.

Asafetida

Asafetida is a strong-smelling spice made from a plant resin, used in tiny pinches in Indian cooking. Raw it smells sharp, and cooked in fat it mellows into a savory, onion-and-garlic-like flavor. It is sometimes used to replace onion and garlic in Autoimmune Protocol cooking, though not everyone tolerates it.

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Ashwagandha

Ashwagandha is a root from a plant in the nightshade family, used in Ayurvedic tradition and taken today as a supplement to support the stress response. Because it belongs to the nightshade family, it is grouped with nightshades on elimination lists and is typically avoided during the strict phase of the Autoimmune Protocol.

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Atemoya

Atemoya is a tropical fruit created by crossing the cherimoya and the sugar apple, with soft, creamy, custard-like flesh and a sweet, slightly tangy flavor. It is eaten fresh with a spoon once fully ripe. The seeds and skin are not eaten.

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Autoantigen

An autoantigen is a piece of the body's own tissue that the immune system mistakenly treats as foreign and builds a response against. In autoimmune thyroid disease, thyroid proteins act as the autoantigen the immune system targets. Identifying the specific autoantigen in a given condition helps explain which tissue bears the brunt of the attack.

Reference: Molecular mimicry and autoimmunity. (Journal of autoimmunity, 2018) via PubMed

Autoimmune disease

Autoimmune disease is a condition in which the immune system, built to defend the body against infection, turns and attacks the body's own tissue instead. Many autoimmune conditions exist, each targeting different organs, from the thyroid to the joints to the gut lining. Genetics, gut health, stress, and environmental triggers all play a role.

Reference: Pathogenesis of autoimmune disease. (Nature reviews. Nephrology, 2023) via PubMed

B cell

A B cell is a type of white blood cell that produces antibodies, the proteins that tag pathogens for the rest of the immune system to act on. Some B cells become long-lived memory cells that recognize the same target quickly next time. In autoimmune disease, B cells can end up producing antibodies against the body's own tissue.

Reference: B-cell depletion in autoimmune diseases. (Annals of the rheumatic diseases, 2024) via PubMed

Bacon fat

Bacon fat is the rendered fat left in the pan after cooking bacon, strained and saved for later use. It carries a smoky, savory flavor that works well for sauteing vegetables or starting a soup base. Choosing bacon from a trusted source matters more than the fat itself.

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Bamboo shoot

Bamboo shoots are the young, tender shoots of the bamboo plant, harvested before they toughen and turn woody. They are always cooked before eating, since raw bamboo shoots contain compounds that need heat to neutralize. Sliced or shredded, they show up in stir-fries, soups, and braised dishes across Asian cooking.

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Banana flower

Banana flower, also called banana blossom, is the large purple blossom that forms at the end of a banana bunch. The tough outer petals are discarded and the pale, tender inner layers are sliced and cooked, often soaked in acidic water first to prevent browning. It has a slightly bitter, artichoke-like flavor.

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Banana stem

Banana stem is the fibrous inner core of the banana plant's trunk, not the fruit itself. It is sliced very thin, soaked to remove excess sap, and cooked into soups, salads, and stir-fries in South Asian and Southeast Asian cooking. It has a mild, slightly crunchy texture.

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Barbacoa

Barbacoa is a traditional method of slow-cooking meat, originally in a pit covered with maguey leaves, until it becomes tender enough to shred. Modern versions use a slow cooker or oven instead. The meat is seasoned simply and can easily be made without nightshade spices for the Autoimmune Protocol.

Batch cooking

Batch cooking means preparing a larger quantity of food in one session and portioning it out for meals across the week, rather than cooking from scratch every day. It is especially useful on a restrictive way of eating, where fewer convenience options exist. A few hours on one day can cover several days of meals.

Beta-carotene

Beta-carotene is an orange-red pigment found in carrots, sweet potato, and other orange and dark leafy produce. The body can convert it into vitamin A as needed, which makes it a useful plant-based source of that nutrient. It is best absorbed when eaten with some fat.

Beta-glucan

Beta-glucan is a type of fiber found in mushrooms, oats, and barley that has the ability to stimulate immune cell activity. That immune-stimulating effect can be useful in some contexts and unhelpful for someone whose immune system is already overactive, which is why high-beta-glucan foods like mushrooms are sometimes limited on the Autoimmune Protocol.

Reference: β-1,3/1,6-Glucans and Immunity: State of the Art and Future Directions. (Molecular nutrition & food research, 2020) via PubMed

Bilberry

Bilberry is a small, dark blue wild berry closely related to the blueberry, with a similar tart, slightly sweet flavor. It grows wild across Europe and has a long history of traditional use for eye and circulatory health. It can be used in the same way as blueberries in recipes.

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Bile

Bile is a digestive fluid made by the liver and stored in the gallbladder, released into the small intestine to help break down and absorb dietary fat. Without enough bile flow, fat-soluble nutrients like vitamins A, D, E, and K become harder to absorb. Gallbladder or liver issues can affect how well this process works.

Bioavailability

Bioavailability is a measure of how much of a nutrient or medication the body actually absorbs and can use, rather than how much is simply present in a food or dose. It can vary between whole food sources, supplement forms, and even between brands of the same medication.

Bioidentical hormones

Bioidentical hormones are hormone preparations made to match the exact molecular structure of the hormones the body naturally produces, as opposed to some synthetic hormone medications that are structurally different. They can be compounded individually or come in regulated pharmaceutical forms. Whether one form suits a person better than another is an individual medical decision.

Reference: Compounded Bioidentical Menopausal Hormone Therapy: ACOG Clinical Consensus No. 6. (Obstetrics and gynecology, 2023) via PubMed

Bitter melon

Bitter melon is a bumpy, pale green gourd with a strongly bitter taste, common in Asian and South Asian cooking. The white pith and seeds inside are scooped out before cooking to soften the bitterness somewhat. It is often salted and rested, then stir-fried or simmered into curries.

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Black caraway

Black caraway, also called nigella or black cumin, is a small, dark, teardrop-shaped seed with a peppery, slightly onion-like flavor when toasted. It is scattered over breads in some cuisines and used whole in spice blends. It is unrelated to true caraway seed despite the shared name.

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Black sapote

Black sapote, sometimes called chocolate pudding fruit, is a tropical fruit that looks green on the outside and, once fully ripe, has soft brown flesh with a texture close to pudding. It is eaten with a spoon straight from the skin. Underripe fruit is astringent and unpleasant, so ripeness matters.

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Blanch

To blanch is to drop a vegetable into boiling water briefly, then immediately transfer it to ice water to stop the cooking. It sets bright color, softens texture slightly, and is often a first step before freezing vegetables for storage. Blanching times are usually short, just long enough to take the raw edge off.

Blastocystis hominis

Blastocystis hominis is a single-celled organism sometimes found in stool testing. It is present in many people without causing problems, but in higher amounts it has been linked to gut inflammation, immune activation, and digestive symptoms like bloating and irregular bowel habits. Whether it needs treatment depends on symptoms and the overall gut picture, not the finding alone.

Reference: Modulating the Gut Micro-Environment in the Treatment of Intestinal Parasites. (Journal of clinical medicine, 2016) via PubMed

Blood orange

Blood orange is a variety of orange with deep red flesh and a flavor that carries a hint of berry alongside the usual citrus sweetness. The red color comes from anthocyanin pigments not found in most other citrus. It can be eaten out of hand or juiced.

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Blood-brain barrier

The blood-brain barrier is a tightly regulated layer of cells that controls what passes from the bloodstream into brain tissue, screening out many toxins and pathogens while letting needed nutrients through. In some autoimmune and inflammatory conditions this barrier becomes more permeable, one proposed link between systemic inflammation and symptoms like brain fog.

Reference: A blood-brain barrier overview on structure, function, impairment, and biomarkers of integrity. (Fluids and barriers of the CNS, 2020) via PubMed

Bone broth

Bone broth is made by simmering animal bones, often with joints or connective tissue attached, until minerals and proteins leach into the liquid. It provides amino acids like glycine and proline, building blocks used in connective tissue and the gut lining. It is a staple on the Autoimmune Protocol, not a stand-alone fix for gut issues.

Bone density

Bone density is a measure of how much mineral is packed into a given area of bone, most often checked with a DEXA scan. Density alone does not capture the full picture of bone strength or internal structure. Thyroid hormone levels and long-term steroid use are two factors relevant to bone density in autoimmune care.

Reference: Role of Thyroid Hormones in Skeletal Development and Bone Maintenance. (Endocrine reviews, 2016) via PubMed

Bone turnover

Bone turnover is the ongoing cycle in which old bone tissue is broken down and new bone is built to replace it. The pace of this cycle shifts with hormone levels, and thyroid hormone in particular influences how fast it runs, which matters for anyone managing thyroid-related autoimmune disease.

Reference: The bone remodelling cycle. (Annals of clinical biochemistry, 2018) via PubMed

Bottle gourd

Bottle gourd, also known as opo, lauki, or calabash, is a pale green gourd with mild, watery flesh. It is peeled and cooked into curries, soups, and stir-fries across South Asian and Southeast Asian cooking, taking on the flavor of whatever it is cooked with. It is rarely eaten raw.

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BPA

BPA, short for bisphenol A, is a chemical used in some plastics and in the lining of certain food and beverage cans. It can act like a weak estrogen once absorbed, which places it among the endocrine disruptors people are often advised to reduce exposure to.

Reference: Bisphenol A and its analogues in thyroid diseases: Evidence from dysfunction, autoimmunity, and cancer. (iScience, 2026) via PubMed

Braise

To braise is to cook food slowly in a small amount of liquid in a covered pot, usually starting with a sear and finishing low and slow in the oven or on the stovetop. It is the method that turns tougher cuts of meat tender. Root vegetables and hearty greens braise well too.

Brassica (cruciferous)

Brassica, also called cruciferous vegetables, is the plant family that includes broccoli, cauliflower, cabbage, kale, bok choy, and their many relatives. These vegetables contain compounds that support the body's detoxification pathways. Some people with thyroid conditions are advised to cook rather than eat them raw in large amounts, since raw cruciferous vegetables can affect iodine uptake.

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Breadfruit

Breadfruit is a large, starchy tropical fruit that is treated like a vegetable in cooking. Unripe, it is firm and mild, roasted, boiled, or fried much like a potato, and as it ripens the flesh turns soft and noticeably sweeter. It grows on trees across the Pacific, Caribbean, and parts of Africa.

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Brine

To brine is to soak meat, poultry, or vegetables in a salted water solution before cooking, sometimes with added aromatics. The salt draws moisture into the food and seasons it from the inside, which helps keep lean cuts like chicken breast juicy through cooking. Brining times range from a short soak to overnight depending on the cut.

Broccoli rabe

Broccoli rabe, also called rapini, is a leafy green vegetable with small broccoli-like buds, thin stalks, and a pleasantly bitter edge. It is popular in Italian cooking, usually sauteed with garlic and olive oil or blanched first to soften the bitterness. The whole plant, leaves, stems, and buds, is edible.

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Broccolini

Broccolini is a cross between broccoli and Chinese broccoli, with long, slender stalks and small, loose florets on top. Sometimes called baby broccoli, it has a milder, slightly sweeter flavor than regular broccoli and cooks quickly. It is good roasted, sauteed, or steamed whole, stem and floret together.

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Broil

To broil is to cook food using intense direct heat from above, usually the top element of an oven, with the food placed close underneath. It browns and crisps the surface quickly, useful for finishing a dish or charring vegetables. Because the heat is so direct, food needs close watching to avoid burning.

Buddha's hand

Buddha's hand is a citrus fruit that grows in strange, finger-like sections branching out from a central base, with almost no pulp or juice inside. What it offers instead is fragrant peel, used for zest in cooking and baking or simply for scent. It is prized more for aroma than for eating out of hand.

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Bulgogi

Bulgogi is a Korean dish of thinly sliced beef marinated in a sweet and savory sauce, traditionally built on soy sauce, pear, garlic, and sesame, then quickly grilled or pan-seared. The marinade both flavors and tenderizes the meat. An Autoimmune Protocol version swaps in coconut aminos and skips the sesame and soy.

Bulgur

Bulgur is a quick-cooking form of wheat that has been parboiled, dried, and cracked into small pieces, most familiar as the base of tabbouleh. Because it is a wheat product, it contains gluten and is not used on the Autoimmune Protocol. It cooks faster than most whole grains since it only needs a brief soak or simmer.

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Burdock

Burdock is a long, slender root vegetable with tough brown skin and an earthy, slightly sweet flavor, known in Japanese cooking as gobo. It is scraped or peeled, then sliced and simmered, braised, or stir-fried, often alongside carrot in dishes like kinpira. It has a satisfying, fibrous crunch even after cooking.

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Butyrate

Butyrate is a short-chain fatty acid produced when gut bacteria ferment fiber from food. It is the preferred fuel source for the cells lining the colon and plays a role in keeping the gut barrier intact and calming inflammation locally. Eating a variety of fiber-containing foods is one way to support the bacteria that produce it.

Reference: Short-chain fatty acids: linking diet, the microbiome and immunity. (Nature reviews. Immunology, 2024) via PubMed

C-reactive protein (CRP)

C-reactive protein, or CRP, is a protein made by the liver that rises in the blood when inflammation is present in the body. It is a commonly used marker of general inflammatory activity, though it does not point to a specific cause or location. It is usually checked alongside other labs, not read alone.

Reference: C-reactive protein: a target for therapy to reduce inflammation. (Frontiers in immunology, 2023) via PubMed

Cacao

Cacao is the raw bean that chocolate and cocoa powder are made from, before roasting and processing strip away some of its natural compounds. It contains polyphenols and minerals such as magnesium and iron. On a strict elimination phase of the Autoimmune Protocol it is typically avoided, since it is a seed-based food.

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Calamansi

Calamansi, also called calamondin, is a small, sour citrus fruit central to Filipino cooking. Its juice works much like lime juice, adding brightness to marinades, dressings, and drinks.

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Callaloo

Callaloo refers to leafy greens, most often amaranth or taro leaves, and also names the classic Caribbean stewed dish made from them. The leaves are a good source of vitamins A and C and are typically cooked rather than eaten raw.

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Calprotectin

Calprotectin is a protein released by white blood cells when the gut lining is actively inflamed. A stool test that measures calprotectin helps tell inflammatory bowel disease apart from other digestive complaints, which matters when sorting out whether gut symptoms point toward an autoimmune process.

Reference: Clinical value of fecal calprotectin. (Critical reviews in clinical laboratory sciences, 2019) via PubMed

Camu camu

Camu camu is a small, tart Amazonian berry usually sold as a freeze-dried powder since the fresh fruit does not travel well. It carries one of the highest known concentrations of vitamin C of any food, and is often added to smoothies and tonics.

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Candida

Candida is a yeast that lives in small, normal amounts in the gut and on the skin. Under conditions such as antibiotic use, high sugar intake, or a weakened immune system it can overgrow, and that overgrowth has been linked to gut barrier disruption and immune activation relevant to autoimmune disease.

Reference: Clinical Significance of Intestinal Fungal Overgrowth: Integrating the Gut Mycobiome into Modern Gastroenterology. (Microorganisms, 2026) via PubMed

Canistel

Canistel, also called egg fruit, is a tropical fruit with sweet, dense flesh that resembles a cooked egg yolk in texture and color. It is eaten ripe and raw, or blended into smoothies and desserts.

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Capers

Capers are the small, unopened flower buds of the caper bush, cured in salt or brine before use. They add a salty, tangy burst of flavor to sauces, salads, and fish dishes.

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Capsicum

Capsicum is the botanical name for the pepper family, which includes bell peppers and chili peppers. All capsicums are nightshades and are commonly removed during the early phase of the Autoimmune Protocol.

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Caramelize

To caramelize means to cook food slowly, often onions or other vegetables, until their natural sugars break down and brown, producing a deep, sweet flavor. Low heat and patience are what separate true caramelizing from simply browning.

Cardoon

Cardoon is a vegetable related to the artichoke, with long, celery-like stalks that carry an artichoke flavor. The stalks need to be peeled and cooked, usually braised or simmered, since they are tough and bitter raw.

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Carob

Carob is a naturally sweet powder ground from the dried pods of the carob tree, used as a caffeine-free stand-in for chocolate in baking and drinks. Unlike cacao it is not a seed, so it is generally treated as friendly on the Autoimmune Protocol in moderation.

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Carrier proteins (binding globulins)

Carrier proteins, also called binding globulins, are proteins in the blood that attach to hormones and transport them through the bloodstream. Hormone bound to a carrier is inactive, so lab work often measures 'free' hormone separately, which matters for accurately reading thyroid and sex hormone panels during an autoimmune workup.

Reference: A Reappraisal of Testosterone's Binding in Circulation: Physiological and Clinical Implications. (Endocrine reviews, 2017) via PubMed

Casein

Casein is the main protein found in dairy. Its molecular structure closely resembles gluten, which means the immune system can mistake one for the other, a pattern called cross-reactivity that is especially relevant for people with celiac disease or gluten sensitivity.

Reference: Beneficial Effects of Milk Having A2 β-Casein Protein: Myth or Reality? (The Journal of nutrition, 2021) via PubMed

Cassava

Cassava, also called yuca, is a starchy tropical root and the source of cassava flour and tapioca. It is a common grain-free staple on the Autoimmune Protocol and must always be cooked fully, since the raw root contains compounds that are toxic.

Cassava flour

Cassava flour is a grain-free flour milled from the whole cassava root, distinct from tapioca starch, which uses only the extracted starch. It behaves similarly to wheat flour in baking, making it a common one-to-one gluten-free substitute.

Cayenne

Cayenne is a hot red chili pepper, most often sold dried and ground into powder. As a nightshade it is typically removed during the elimination phase of the Autoimmune Protocol.

CBC (complete blood count)

A complete blood count, or CBC, is a standard blood panel that measures red blood cells, white blood cells, and platelets. It screens for anemia, infection, and other patterns, and is often one of the first tests run when investigating fatigue or a suspected autoimmune condition.

Reference: Anemia: Evaluation and Diagnostic Tests. (The Medical clinics of North America, 2016) via PubMed

Celeriac

Celeriac, also called celery root, is the knobby root of a variety of celery grown for its bulb rather than its stalks. It has a mild, earthy celery flavor and is roasted, mashed, or added to soups.

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Celiac disease

Celiac disease is an autoimmune condition in which eating gluten triggers the immune system to attack and damage the lining of the small intestine. The only established management is strict, lifelong avoidance of gluten, and untreated celiac disease raises the risk of nutrient deficiencies and other autoimmune conditions.

Reference: Advances in the pathophysiology, diagnosis, and management of celiac disease. (BMJ, 2025) via PubMed

Chanterelle

Chanterelles are golden, trumpet-shaped wild mushrooms with a delicate flavor often described as fruity or peppery. They are prized in cooking and typically sauteed in butter or oil.

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Chayote

Chayote is a pale green, pear-shaped gourd with crisp, mild flesh. It can be eaten raw in salads or cooked in soups and stir-fries, much like summer squash.

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Cherimoya

Cherimoya is a sweet, creamy tropical fruit with soft white flesh and large black seeds that are not eaten. Its flavor is often described as a blend of banana, pineapple, and pear.

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Chervil

Chervil is a delicate herb with a mild flavor that blends parsley and anise. Because heat destroys its flavor quickly, it is usually added at the very end of cooking.

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Chicory

Chicory is a leafy plant with a slightly bitter edge, eaten raw in salads or cooked like other greens. Its root is roasted and ground as a caffeine-free coffee substitute.

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Chimichurri

Chimichurri is a fresh, uncooked sauce of finely chopped herbs, garlic, oil, and vinegar, traditional in Argentine cooking. It is spooned over grilled meats and vegetables to add brightness and acidity.

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Chinese broccoli

Chinese broccoli, also called gai lan, is a leafy green vegetable with thick stems, dark leaves, and small white flower buds. It is typically steamed or stir-fried and has a flavor similar to broccoli with a pleasant bitterness.

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Chinese yam

Chinese yam, also called nagaimo or mountain yam, is a mild, starchy tuber used in East Asian cooking. It has a distinctive sticky texture when grated raw and can also be sliced and cooked.

See also: On the food list

Cholecalciferol (vitamin D3)

Cholecalciferol, or vitamin D3, is the form of vitamin D the skin produces from sun exposure and the form most often used in supplements. It generally raises blood vitamin D levels more effectively than vitamin D2, and adequate vitamin D status is closely tied to immune regulation, which makes it a frequent focus in autoimmune care.

Reference: Regulation of Immune Function by Vitamin D and Its Use in Diseases of Immunity. (Endocrinology and metabolism clinics of North America, 2017) via PubMed

Choline

Choline is a nutrient the body uses to build cell membranes and support liver and brain function. Egg yolks and liver are among the richest food sources, and adequate choline intake supports healthy liver function, which matters for anyone managing chronic inflammation.

See also: What a proper meal looks like

Reference: Cellular and organismal function of choline metabolism. (Nature metabolism, 2025) via PubMed

Choy sum

Choy sum is a tender Chinese leafy green with slender stems, dark leaves, and small yellow flowers, also known as yu choy. It cooks quickly by steaming or stir-frying and has a mild, slightly sweet flavor.

See also: On the food list

Chrysanthemum greens

Chrysanthemum greens, also called tong ho or shungiku, are the edible leaves of an edible chrysanthemum plant with a distinct aromatic flavor. They are commonly added to soups and hot pots in East Asian cooking.

See also: On the food list

Circadian rhythm

The circadian rhythm is the body's internal roughly day-length clock that governs the timing of sleep, hormone release, and digestion. Consistent light exposure and sleep timing help keep this rhythm steady, and a disrupted circadian rhythm has been linked to increased inflammation and dysregulated immune function.

Reference: Circadian Rhythms in Immunity. (Current allergy and asthma reports, 2020) via PubMed

Cloudberry

Cloudberry is a soft, amber-colored berry that grows in northern climates and has a tart, slightly sweet flavor. It is used in jams, sauces, and traditional Nordic desserts.

See also: On the food list

Coconut aminos

Coconut aminos is a savory, slightly sweet sauce made from fermented coconut sap. It is commonly used as a soy-free substitute for soy sauce in Autoimmune Protocol cooking.

Coconut concentrate

Coconut concentrate, also called coconut butter, is a thick, smooth paste made by pureeing whole coconut meat and its oil together. It adds richness to baked goods and can be melted into sauces and fillings.

See also: On the food list

Coconut cream

Coconut cream is the thick, fatty layer that rises to the top of coconut milk when it separates. It is used to add body and richness to sauces, soups, and dairy-free desserts.

See also: On the food list

Coconut flour

Coconut flour is a grain-free flour made from dried, ground coconut meat after most of the oil has been pressed out. It absorbs liquid heavily, so recipes typically call for only small amounts alongside other ingredients.

Coconut sugar

Coconut sugar is a natural sweetener made from the boiled-down sap of the coconut palm. It is used in place of cane sugar, though it still counts as added sugar and is best kept to small amounts.

See also: On the food list

Coconut syrup

Coconut syrup is a natural liquid sweetener made from coconut sap, similar in use to maple syrup. Like other sweeteners, it is best used sparingly.

See also: On the food list

Coconut vinegar

Coconut vinegar is made from fermented coconut sap or coconut water and has a mild, tangy flavor. It is used in dressings and marinades much like apple cider vinegar.

See also: On the food list

Collagen

Collagen is the most abundant structural protein in the body, forming much of the skin, joints, and the lining of the gut. Bone broth and connective cuts of meat supply dietary collagen, and supporting collagen production is often part of gut healing approaches since the intestinal lining depends on it.

Reference: Collagen Supplementation for Joint Health: The Link between Composition and Scientific Knowledge. (Nutrients, 2023) via PubMed

Collagen peptides

Collagen peptides are a flavorless protein powder made by breaking down animal connective tissue into pieces small enough to dissolve fully in hot or cold liquid. They are added to coffee, smoothies, and soups as an easy way to increase daily collagen intake.

See also: On the food list

Combination therapy (T4/T3)

Combination therapy refers to a thyroid treatment approach that provides both T4 and T3 hormone, rather than T4 alone as in standard levothyroxine treatment. Some prescribers turn to it when a person's symptoms persist despite normal lab values on T4 alone, which can happen when the body converts T4 to active T3 poorly.

Reference: Treatment Preferences in Patients With Hypothyroidism. (The Journal of clinical endocrinology and metabolism, 2025) via PubMed

Comorbidity

A comorbidity is a second health condition that occurs alongside a primary one. Autoimmune conditions frequently cluster together, so having one autoimmune diagnosis raises the likelihood of developing another over time.

Reference: Autoimmune endocrine diseases. (Minerva endocrinologica, 2017) via PubMed

Comprehensive stool analysis

A comprehensive stool analysis is a laboratory test that examines a stool sample for the balance of gut bacteria, markers of inflammation, signs of infection, and how well food is being digested and absorbed. It gives a detailed picture of gut health that can guide healing strategies for someone with digestive or autoimmune symptoms.

Reference: Luminally expressed gastrointestinal biomarkers. (Expert review of gastroenterology & hepatology, 2017) via PubMed

Corpus luteum

The corpus luteum is a temporary gland that forms in the ovary from the follicle left behind after ovulation. It produces progesterone through the second half of the menstrual cycle, and progesterone has calming effects on the immune system that matter for anyone tracking symptom flares against their cycle.

Reference: Immune cells in the corpus luteum: friends or foes? (Reproduction (Cambridge, England), 2001) via PubMed

Cortisol

Cortisol is a hormone produced by the adrenal glands that helps regulate the stress response, blood sugar, and inflammation. It normally rises in the morning and tapers through the day, and chronically elevated or disrupted cortisol patterns are linked to the immune dysregulation seen in autoimmune disease.

Reference: Glucocorticoids and chronic inflammation. (Rheumatology (Oxford, England), 2016) via PubMed

Cortisol awakening response

The cortisol awakening response is the sharp rise in cortisol that occurs in the first half hour after waking, which helps establish energy and alertness for the day. An abnormal awakening response, either blunted or exaggerated, is often used as a marker of chronic stress and adrenal dysregulation.

Reference: Evaluation and update of the expert consensus guidelines for the assessment of the cortisol awakening response (CAR). (Psychoneuroendocrinology, 2022) via PubMed

Cream of tartar

Cream of tartar is a fine white powder, a byproduct of winemaking, used in baking to stabilize whipped egg whites and, paired with baking soda, to help batters rise. It also keeps sugar syrups from crystallizing.

See also: On the food list

Cremini

Cremini mushrooms are brown button mushrooms with a firmer texture and deeper, earthier flavor than standard white mushrooms. Left to mature fully, the same mushroom becomes a portobello.

See also: On the food list

Crohn's disease

Crohn's disease is a form of inflammatory bowel disease that can affect any part of the digestive tract, often in patches, and can inflame the full thickness of the intestinal wall. It causes symptoms such as pain, diarrhea, and fatigue, and diet and lifestyle changes are often used alongside medical treatment to help manage flares.

Reference: Crohn's disease. (Lancet (London, England), 2016) via PubMed

Cross-reactivity

Cross-reactivity happens when the immune system, already primed to react against one protein such as gluten, also attacks a second protein because its structure looks similar. Casein in dairy is the most well-documented gluten cross-reactor, which is why some people with gluten sensitivity also react to dairy.

Reference: Molecular mimicry and autoimmunity. (Journal of autoimmunity, 2018) via PubMed

Cucurbitaceae

Cucurbitaceae is the botanical family of gourd vegetables, which includes cucumber, squash, melon, zucchini, and Asian gourds such as bottle gourd and ridge gourd. Knowing the family helps with rotating foods and spotting patterns in reactions.

See also: On the food list

Culantro

Culantro, also called recao or sawtooth coriander, is a pungent herb with a flavor similar to cilantro but considerably stronger. It is common in Caribbean and Latin American cooking, especially in slow-cooked dishes where its flavor holds up to heat.

See also: On the food list

Cure

To cure means to preserve and firm meat or fish using salt and sometimes sugar or other seasonings, rather than cooking it with heat. Bacon, gravlax, and salt-cured olives are all examples of cured foods.

Currant

Currants are tiny, tart berries that come in red, black, and white varieties, used fresh or cooked into jams, sauces, and baked goods. They are distinct from the small dried grapes sold under the same name.

See also: On the food list

Curry leaf

Curry leaf is a fragrant leaf used throughout South Indian cooking, typically added whole to hot oil at the start of cooking to release its aroma. Despite the name, it is not related to curry powder.

See also: On the food list

Cytokine

A cytokine is a small signaling protein released by immune cells that helps direct inflammation and coordinate the wider immune response. Some cytokines drive inflammation while others calm it, and the balance between the two is central to understanding how autoimmune disease develops and flares.

Reference: Pro- versus anti-inflammatory cytokines: myth or reality. (Cellular and molecular biology (Noisy-le-Grand, France), 2001) via PubMed

Cytotoxic T cell

A cytotoxic T cell is a type of immune cell that directly destroys other cells it identifies as infected or abnormal. In autoimmune disease this same destructive machinery can mistakenly target healthy tissue, contributing to the organ or tissue damage seen in these conditions.

Reference: Immune aging - A mechanism in autoimmune disease. (Seminars in immunology, 2023) via PubMed

Daikon

Daikon is a large, mild white radish widely used in Asian cooking. It can be eaten raw in salads, pickled, or simmered in soups and stews.

See also: On the food list

Dairy-protein isolate

Dairy-protein isolate refers to a concentrated dairy protein, such as whey or casein powder, extracted and added to many packaged and processed foods. Reading ingredient labels closely is the only reliable way to catch it, since it often hides under general terms.

See also: On the food list

Dandy Blend

Dandy Blend is a brand-name caffeine-free beverage made from roasted dandelion root, chicory root, and other roasted plant ingredients. It brews and tastes similar to instant coffee and is a common coffee substitute on the Autoimmune Protocol.

See also: On the food list

DAO (diamine oxidase)

DAO, or diamine oxidase, is an enzyme made mostly in the lining of the gut that breaks down histamine from food before it can build up in the bloodstream. Low DAO activity, often tied to gut lining damage, is associated with histamine intolerance and the wide range of symptoms that come with it.

Reference: Histamine and histamine intolerance. (The American journal of clinical nutrition, 2007) via PubMed

Deglaze

To deglaze means to add liquid, such as broth or vinegar, to a hot pan after searing meat and scrape up the browned bits stuck to the bottom. Those browned bits carry concentrated flavor and become the base of a pan sauce.

Deiodinase enzymes

Deiodinase enzymes convert the storage thyroid hormone T4 into the active hormone T3, or in some cases into inactive reverse T3. These enzymes depend on nutrients such as selenium and zinc to function well, which is one reason nutrient status matters so much in thyroid-related autoimmune conditions like Hashimoto's.

Reference: Deiodinases: the balance of thyroid hormone: local control of thyroid hormone action: role of type 2 deiodinase. (The Journal of endocrinology, 2011) via PubMed

Delicata squash

Delicata squash is a small, oblong winter squash with cream and green striped skin and sweet, tender flesh. Unlike most winter squash its skin is thin enough to eat, which makes it easy to simply slice and roast.

See also: On the food list

Dendritic cell

A dendritic cell is an immune cell that captures and samples foreign material, then presents it to other immune cells to help decide whether to launch a response. Dendritic cells play a key role in the earliest steps of an immune reaction, including the missteps that can set autoimmune disease in motion.

Reference: Self-antigen presentation by dendritic cells in autoimmunity. (Frontiers in immunology, 2014) via PubMed

Detoxification

Detoxification is the body's ongoing process, carried out mainly by the liver, kidneys, and gut, of transforming and clearing waste products, hormones, and toxins. Supporting these normal pathways through nutrients such as B vitamins, adequate fiber, and hydration is a common focus in autoimmune care, though the body carries out this process on its own.

Reference: Detoxification pathways in the liver. (Journal of inherited metabolic disease, 1991) via PubMed

DEXA scan

A DEXA scan is an imaging test that measures bone mineral density using low-dose X-rays. It is a standard tool for diagnosing osteoporosis and tracking bone health, which matters for anyone on long-term steroid treatment or with an autoimmune condition that affects bone density.

Reference: Update on Osteoporosis Screening and Management. (The Medical clinics of North America, 2021) via PubMed

DHEA (dehydroepiandrosterone)

DHEA is a hormone produced by the adrenal glands that serves as a raw material the body converts into estrogen and testosterone. Levels tend to decline with chronic stress and age, and DHEA is often measured as part of assessing adrenal function and stress resilience.

Reference: Dehydroepiandrosterone (DHEA): Pharmacological Effects and Potential Therapeutic Application. (Mini reviews in medicinal chemistry, 2023) via PubMed

DHEA-S (DHEA sulfate)

DHEA-S is the sulfated storage form of DHEA that circulates in the blood at much higher and steadier levels than DHEA itself. Because it stays more stable throughout the day, it is the form most labs measure to estimate adrenal reserve.

Reference: DHEA and DHEA-S: a review. (Journal of clinical pharmacology, 1999) via PubMed

Digestive enzymes

Digestive enzymes are proteins made by the salivary glands, stomach, pancreas, and small intestine that break food down into pieces small enough for the body to absorb. Impaired enzyme production, which can accompany chronic gut inflammation, may contribute to poor nutrient absorption and ongoing digestive symptoms.

Reference: Efficacy of pancreatic enzyme replacement therapy in chronic pancreatitis: systematic review and meta-analysis. (Gut, 2016) via PubMed

Diurnal cortisol rhythm

The diurnal cortisol rhythm is the body's normal daily cortisol pattern, high soon after waking and low at night. A saliva test checks several points across the day to map this curve rather than relying on one blood draw. A flattened pattern is one marker clinicians use when assessing chronic stress and fatigue in autoimmune disease.

Reference: Diurnal cortisol slopes and mental and physical health outcomes: A systematic review and meta-analysis. (Psychoneuroendocrinology, 2017) via PubMed

DNA methylation

DNA methylation is an epigenetic process that attaches small chemical tags to DNA, switching genes on or off without altering the genetic code itself. Nutrients like folate and vitamin B12 support this process. Because methylation patterns shift with diet, stress, and toxin exposure, they are studied as one pathway linking environment to autoimmune disease risk.

Reference: Exposome: Epigenetics and autoimmune diseases. (Autoimmunity reviews, 2024) via PubMed

Dragonfruit

Dragonfruit is a tropical fruit with bright pink or yellow skin and mildly sweet white or red flesh flecked with tiny black seeds. It is a source of vitamin C and fiber and works well blended into smoothies or eaten plain as a Core Autoimmune Protocol fruit.

See also: On the food list

Dredge

To dredge means to lightly coat a piece of food, often meat or fish, in flour, starch, or breading before searing or frying. On the Autoimmune Protocol, arrowroot or cassava flour stands in for wheat flour to create the same crisp, browned surface.

Drumstick pod

The drumstick pod is the long green seed pod of the moringa tree, also called moringa pod. Cooks simmer it in soups and curries until tender, then scrape out the soft pulp and seeds inside, leaving the tough outer fiber behind. It is valued for its vitamin and mineral content.

See also: On the food list

Drupe

A drupe is the botanical term for a fruit built around a single hard pit or stone, such as a peach, plum, olive, or mango. Knowing the category is useful in the kitchen, since drupes are typically halved and pitted rather than cored or seeded like other fruit.

Dulse

Dulse is a soft, reddish-purple sea vegetable with a naturally salty, savory flavor. It is sold dried as flakes or strips and can be sprinkled over cooked vegetables or fish as a seasoning, contributing iodine and trace minerals.

See also: On the food list

Durian

Durian is a large, spiky tropical fruit known for its strong odor and rich, custard-like flesh. Southeast Asian markets sell it fresh or frozen, and it is eaten plain as a Core Autoimmune Protocol fruit, though the smell keeps it out of many kitchens.

See also: On the food list

DUTCH test

The DUTCH test, short for Dried Urine Test for Comprehensive Hormones, measures cortisol and sex hormone byproducts from a series of dried urine samples collected across a day. It maps hormone production and clearance in more detail than a single blood draw, useful for tracing patterns behind fatigue, cycle irregularity, and stress load.

Dysbiosis

Dysbiosis is an imbalance in the gut microbiome, meaning too few beneficial bacteria, an overgrowth of less helpful species, or a general loss of diversity. It is linked to increased intestinal permeability and immune activation, which is part of why gut health is a central focus in autoimmune disease management.

Reference: Gut Dysbiosis and Fecal Microbiota Transplantation in Autoimmune Diseases. (International journal of molecular sciences, 2022) via PubMed

Edamame

Edamame are immature green soybeans, usually steamed or boiled in the pod and eaten as a snack or side dish. As a soy food, edamame is set aside during the elimination phase of the Autoimmune Protocol along with other legumes.

Einkorn

Einkorn is an ancient variety of wheat, often marketed as easier to digest because of its simpler gluten structure. It still contains gluten, however, so it remains off the table during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Elderberry

Elderberry is a small, dark purple berry traditionally simmered into syrup or tea. Raw elderberries and unripe parts of the plant are mildly toxic, so the berries must always be cooked before eating, and elderberry syrup is a common addition to a Core Autoimmune Protocol pantry.

See also: On the food list

Electrolyte

Electrolytes are minerals such as sodium, potassium, and magnesium that carry an electrical charge in body fluids and are essential for nerve signaling, muscle contraction, and hydration. Getting enough of them matters on any elimination diet, since cutting processed foods can also cut a habitual sodium source.

Elimination phase (Core)

The elimination phase, sometimes called the Core phase, is the opening stretch of the Autoimmune Protocol, when every potentially provoking food group is removed and meals are built from the Core 'yes' list only. Research on this type of elimination diet has shown improvement in reported symptoms for some people with inflammatory bowel disease.

Reference: Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. (Inflammatory bowel diseases, 2017) via PubMed

Elimination-provocation (AEP)

Elimination-provocation, sometimes abbreviated AEP, is Datis Kharrazian's term for the two-part process behind the Autoimmune Protocol: foods are removed during the elimination phase, then reintroduced one at a time during the provocation phase to see which ones trigger a reaction. The pattern of response guides the long-term food list.

Emulsifier

An emulsifier is a food additive, such as lecithin, polysorbate, or carrageenan, that keeps ingredients like oil and water from separating in processed foods. Some research on emulsifiers has linked them to changes in gut bacteria and increased intestinal permeability, which is why they are avoided on the Autoimmune Protocol.

Reference: Ultra-processed foods and food additives in gut health and disease. (Nature reviews. Gastroenterology & hepatology, 2024) via PubMed

Emulsify

To emulsify means to blend two liquids that would normally separate, such as oil and vinegar, into one smooth, stable mixture, often by whisking slowly or adding a binder like mustard. Homemade Autoimmune Protocol mayonnaise and salad dressings both rely on this technique.

En papillote

En papillote is a French cooking method in which food, often fish or vegetables, is sealed inside a parchment paper packet and baked so it steams gently in its own juices. It keeps food moist without added fat and works well for delicate proteins on the Autoimmune Protocol.

Endocrine disruptor

An endocrine disruptor is a chemical from the environment, such as BPA, phthalates, or certain pesticides, that can interfere with normal hormone signaling in the body. Because hormone balance and immune function are closely linked, reducing exposure to these chemicals is one piece of the broader lifestyle approach used alongside diet.

Reference: Endocrine-disrupting chemicals and autoimmune diseases. (Environmental research, 2023) via PubMed

Endometriosis

Endometriosis is a condition in which tissue similar to the uterine lining grows outside the uterus, causing pain, inflammation, and sometimes fertility problems. It is increasingly studied alongside autoimmune disease because of shared patterns of chronic inflammation and immune dysregulation, and it often coexists with conditions like Hashimoto's thyroiditis.

Reference: Endometriosis and autoimmunity. (Autoimmunity reviews, 2025) via PubMed

Endotoxin

An endotoxin is a toxic compound, most often lipopolysaccharide, released from the outer wall of certain gut bacteria, particularly as they die off. When it crosses a compromised gut lining into the bloodstream it can trigger a strong inflammatory response, a process studied under the name metabolic endotoxemia.

Reference: Role of Metabolic Endotoxemia in Systemic Inflammation and Potential Interventions. (Frontiers in immunology, 2021) via PubMed

Enterocyte

An enterocyte is one of the cells lining the small intestine responsible for absorbing nutrients and forming the gut's protective barrier. These cells rely heavily on the amino acid glutamine for fuel and repair, part of why gut-healing protocols often include glutamine-rich foods like bone broth.

Reference: Intestinal Barrier Dysfunction in Inflammatory Bowel Disease: Underpinning Pathogenesis and Therapeutics. (Digestive diseases and sciences, 2023) via PubMed

Epazote

Epazote is a pungent Mexican herb with a strong, slightly medicinal aroma, traditionally added to a pot of beans as they cook. It is used sparingly and is often credited, though not proven, with easing the gassiness that beans can cause.

See also: On the food list

Epigenetics

Epigenetics is the study of how gene activity is turned on or off by chemical tags and other markers layered on top of DNA, without changing the genetic sequence itself. Diet, stress, sleep, and toxin exposure all leave epigenetic marks, one reason lifestyle change can shift how autoimmune disease expresses over time.

Reference: Human autoimmune diseases: a comprehensive update. (Journal of internal medicine, 2015) via PubMed

Epstein-Barr virus (EBV)

Epstein-Barr virus is a common virus that most people are infected with at some point and then carry for life in a dormant state. It can reactivate under stress or immune strain, and research has found a strong association between prior Epstein-Barr infection and the later development of certain autoimmune diseases, including multiple sclerosis.

Reference: Epstein-Barr virus as a potentiator of autoimmune diseases. (Nature reviews. Rheumatology, 2024) via PubMed

Erythrocyte sedimentation rate (ESR)

Erythrocyte sedimentation rate, or ESR, is a blood test that measures how quickly red blood cells settle to the bottom of a test tube. A faster rate suggests general inflammation somewhere in the body, though the test does not point to a specific cause or location.

Estradiol

Estradiol is the most active and commonly measured form of estrogen, produced mainly by the ovaries. It plays a central role in the menstrual cycle, bone density, and skin and vaginal tissue health, and levels shift naturally across the cycle and through perimenopause and menopause.

Estrogen

Estrogen is a primary sex hormone, most abundant in women, that regulates the menstrual cycle, supports bone density, and also acts on immune cells throughout the body. Its immune-modulating effects are one reason researchers point to as part of why autoimmune diseases occur far more often in women than in men.

Reference: Immunology and the menstrual cycle. (Autoimmunity reviews, 2011) via PubMed

Estrogen dominance

Estrogen dominance is a functional medicine term for a pattern where estrogen is high relative to progesterone, or where the body clears used estrogen poorly. It is used to describe symptoms like heavy periods, breast tenderness, and mood swings, though it is not a formal diagnosis with a single lab test.

Euthyroid

Euthyroid describes a state in which thyroid hormone levels sit within the standard reference range and the gland is producing an adequate, balanced amount of hormone. A person can be euthyroid on paper while still having Hashimoto's antibodies present, since the two measures track different things.

Fabaceae

Fabaceae is the botanical family name for legumes, the group that includes beans, lentils, peanuts, and soy. On the Autoimmune Protocol the whole family is set aside during the elimination phase because of the proteins and lectins these plants contain.

Farro

Farro is a chewy ancient wheat grain with a nutty flavor, often used in salads and soups. It contains gluten and is grouped with other whole grains kept off the plate during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Fasting insulin

Fasting insulin is a blood test that measures insulin levels after a period without food, usually overnight. Read alongside fasting glucose, it shows how hard the body is working to keep blood sugar steady, and a high result can signal insulin resistance before blood sugar itself becomes abnormal.

Feijoa

Feijoa, also called pineapple guava, is a small green tropical fruit with fragrant, tangy-sweet flesh that tastes something like a mix of pineapple, guava, and mint. It is eaten fresh, scooped from the skin with a spoon, as a Core Autoimmune Protocol fruit.

See also: On the food list

Fennel

Fennel is a crunchy vegetable with a mild licorice-like flavor. The white bulb is sliced raw into salads or roasted until soft and sweet, while the feathery green fronds are chopped and used as an herb for garnish or flavor.

See also: On the food list

Fenugreek

Fenugreek is a small, angular seed spice with a warm, slightly bitter, maple-like flavor, common in Indian cooking and traditional remedies. The fresh leaves are also used as a bitter herb, and both forms are compliant on the Autoimmune Protocol.

See also: On the food list

Fermented foods / probiotics

Fermented foods are foods cultured with beneficial live microbes, such as sauerkraut, coconut kefir, and kombucha, that supply strains of bacteria similar to those found in probiotic supplements. Introducing them gradually is a common way to support a varied gut community during the Autoimmune Protocol.

See also: On the food list

Ferritin

Ferritin is a blood marker that reflects how much iron is stored in the body. Low ferritin often shows up before anemia does on standard blood counts, and iron status affects energy, hair growth, and the conversion of thyroid hormone into its active form.

Fibromyalgia

Fibromyalgia is a chronic condition marked by widespread pain, fatigue, sleep disruption, and tenderness at specific points on the body. It is not itself classified as an autoimmune disease, but it appears more often in people who already have one, and the two are frequently managed together.

Reference: Fibromyalgia: a clinical review. (JAMA, 2014) via PubMed

Fiddlehead fern

Fiddleheads are the young, tightly coiled shoots of the ostrich fern, harvested for a short window in early spring. They must be boiled or steamed thoroughly before eating to remove natural toxins, and their flavor is often compared to asparagus or green beans.

See also: On the food list

Finger lime

Finger lime, sometimes called citrus caviar, is a small elongated citrus fruit whose flesh is made up of tiny round juice vesicles that pop like caviar when bitten. It is used as a bright, tart garnish over fish, salads, or fruit.

See also: On the food list

Fingerroot

Fingerroot, also called krachai or Chinese keys, is a knobby root spice related to ginger and galangal, with a sharp, slightly citrusy, peppery flavor. It shows up in Southeast Asian curries and fish dishes and is used fresh, sliced, or pounded into a paste.

See also: On the food list

Fish sauce

Fish sauce is a salty, deeply savory liquid made by fermenting fish, usually anchovies, with salt over many months. A small amount adds umami depth to soups, marinades, and dipping sauces, and some Autoimmune Protocol brands are made without added sugar or soy.

See also: On the food list

Five-spice

Five-spice is a Chinese seasoning blend, typically combining star anise, clove, cinnamon, fennel, and Sichuan pepper for a warm, sweet, savory flavor. Autoimmune Protocol versions of the blend leave out any nightshade-derived spices such as chili or pepper.

Flare

A flare is a stretch of time when autoimmune disease symptoms noticeably worsen, whether that means more joint pain, fatigue, digestive trouble, or a skin reaction. Flares are often set off by stress, illness, poor sleep, or a food that does not agree, and tracking triggers helps shorten how often they happen.

FODMAPs

FODMAPs are a group of fermentable short-chain carbohydrates, found in foods like garlic, onion, and certain fruits, that can pull water into the gut and ferment quickly, causing gas and bloating in sensitive people. They are a separate framework from the Autoimmune Protocol but are often layered on top of it when SIBO is present.

Reference: Efficacy of a low FODMAP diet in irritable bowel syndrome: systematic review and network meta-analysis. (Gut, 2021) via PubMed

Folate

Folate is a B vitamin needed to build DNA, form red blood cells, and drive methylation reactions throughout the body. It occurs naturally in leafy greens, liver, and legumes, and adequate folate status is part of the broader picture in supporting a well-functioning methylation cycle.

Reference: Causes of vitamin B12 and folate deficiency. (Food and nutrition bulletin, 2008) via PubMed

Folic acid

Folic acid is the synthetic, lab-made form of folate added to fortified flour, cereal, and many supplements. The body has to convert it into an active form before it can be used, a step that some people, particularly those with certain MTHFR gene variants, do less efficiently.

Follicular phase

The follicular phase is the first half of the menstrual cycle, running from the first day of a period until ovulation. During this window a follicle in the ovary matures around a developing egg while estrogen rises, building the uterine lining back up.

Fonio

Fonio is a tiny, quick-cooking West African grain with a mild, nutty flavor similar to couscous. It is a grass-family grain, and like other grains it is set aside during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Free radicals

Free radicals are unstable molecules, produced naturally during metabolism and increased by things like pollution and inflammation, that can damage cells and DNA if left unchecked. The body neutralizes them with antioxidants from food, and an ongoing imbalance between the two, called oxidative stress, is studied in relation to autoimmune disease.

Reference: Free radicals and antioxidants in normal physiological functions and human disease. (The international journal of biochemistry & cell biology, 2006) via PubMed

Free T3

Free T3 is the portion of triiodothyronine circulating unbound to carrier proteins, meaning it is available to enter cells and act on metabolism. It is the active thyroid hormone measured on a full thyroid panel, alongside free T4 and thyroid antibodies.

Free T4

Free T4 is the unbound portion of thyroxine, the storage form of thyroid hormone, that is available for tissues to convert into the more active free T3. Standard thyroid screening often checks only TSH, so requesting free T4 gives a fuller picture of thyroid function.

Free testosterone

Free testosterone is the portion of testosterone not bound to carrier proteins in the blood, meaning it is the fraction actually available for tissues to use. Levels can run low even when a total testosterone result looks normal, which is why both are sometimes measured together.

FSH (follicle-stimulating hormone)

FSH, or follicle-stimulating hormone, is released by the pituitary gland to prompt the ovaries to develop a mature egg-containing follicle each cycle, and in men it supports sperm production. Levels are tracked as part of fertility workups and to assess ovarian reserve approaching menopause.

GABA

GABA is a calming neurotransmitter that lowers nervous system activity and supports relaxation and sleep. Certain strains of gut bacteria produce GABA or influence its signaling, one of the pathways researchers point to when describing the connection between gut health and mood, sometimes called the gut-brain axis.

Reference: Gut Bacteria and Neurotransmitters. (Microorganisms, 2022) via PubMed

Galangal

Galangal is a root spice closely related to ginger but sharper, more citrusy, and harder in texture. It is a staple in Thai and other Southeast Asian dishes, usually sliced thin or pounded into curry paste rather than grated.

See also: On the food list

Garam masala

Garam masala is a warm Indian spice blend, typically built from cumin, coriander, cardamom, cinnamon, and clove, added toward the end of cooking to round out a dish's flavor. Autoimmune Protocol versions leave out any nightshade spices like chili powder or paprika.

Garlic chives

Garlic chives, also called Chinese chives or nira, are flat green leaves with a mild garlic flavor, milder than a garlic clove itself. They are chopped into stir-fries, dumplings, and egg dishes across Asian cooking.

See also: On the food list

Gelatin

Gelatin is a protein extracted from animal bones, skin, and connective tissue that sets liquids into a soft, jelly-like texture when cooled. On the Autoimmune Protocol it is used to thicken sauces, make gummies, and act as a binder in grain-free, egg-free baking.

Gelatin egg

A gelatin egg is an egg substitute made by whisking gelatin into hot water until it blooms, then whipping it once cooled, mimicking the binding power of a beaten egg. It is used in Autoimmune Protocol baking recipes where real eggs are being avoided.

Gene expression

Gene expression is the process of a gene's instructions being read and used to build a protein or carry out a specific function in the cell. Not every gene is active at once, and outside signals, including diet and stress, can turn expression up or down.

Ghee

Ghee is butter that has been simmered until the milk solids separate out and are strained away, leaving pure, golden butterfat behind. Because most of the dairy proteins that provoke reactions are removed in that process, some people who react to butter can tolerate ghee.

Gliadin

Gliadin is one of the two main proteins that make up gluten, and it is the part most responsible for triggering the immune reaction in gluten sensitivity. Gliadin also shares a structural resemblance to thyroid tissue, a phenomenon called molecular mimicry that is studied in relation to Hashimoto's thyroiditis.

Reference: Celiac disease: a comprehensive current review. (BMC medicine, 2019) via PubMed

Glutathione

Glutathione is a molecule made naturally in the body from three amino acids, functioning as one of the main antioxidants used to neutralize free radicals and support the liver's detoxification pathways. Because oxidative stress and impaired detoxification are both features of autoimmune disease, glutathione status is a common area of interest.

Reference: Glutathione synthesis. (Biochimica et biophysica acta, 2012) via PubMed

Gluten

Gluten is a structural protein found in wheat, barley, and rye that gives dough its stretch and chew. It is removed entirely during the elimination phase of the Autoimmune Protocol, along with all grains, because of its association with intestinal permeability.

Glycine

Glycine is an amino acid abundant in bone broth and other collagen-rich foods, and the body uses it to build collagen and support the mucus layer and structure of the gut lining. Adequate glycine intake is one of the nutritional pieces often emphasized in gut-healing protocols.

Reference: Roles of dietary glycine, proline, and hydroxyproline in collagen synthesis and animal growth. (Amino acids, 2017) via PubMed

Glycoalkaloids (e.g. solanine)

Glycoalkaloids, including solanine, are natural defense compounds found in nightshade plants such as potatoes, tomatoes, and eggplant, concentrated especially in green or sprouting potatoes. In sensitive individuals they are thought to irritate the gut lining and contribute to intestinal permeability, which is why nightshades are removed on the Autoimmune Protocol.

Reference: Potato glycoalkaloids adversely affect intestinal permeability and aggravate inflammatory bowel disease. (Inflammatory bowel diseases, 2002) via PubMed

Glyphosate

Glyphosate is the active ingredient in a widely used weed-killer, and residues of it can remain on conventionally grown grains and legumes. Researchers have studied whether chronic low-level exposure affects the gut microbiome and contributes to intestinal permeability, though the evidence is still developing.

Reference: Effects of glyphosate exposure on intestinal microbiota, metabolism and microstructure: a systematic review. (Food & function, 2024) via PubMed

Goiter

A goiter is a visible, palpable enlargement of the thyroid gland, which can be caused by iodine deficiency, Hashimoto's thyroiditis, Graves' disease, or nodules. It is a distinct finding from the transient thyroid swelling some people notice as an autoimmune flare comes and goes.

Goitrogen

A goitrogen is a compound, found especially in raw cruciferous vegetables like broccoli and cabbage, that can interfere with iodine uptake and thyroid hormone production in large, mostly uncooked quantities. Cooking largely deactivates goitrogenic compounds, which is why the Autoimmune Protocol keeps these vegetables and simply recommends cooking them.

Reference: The role of micronutrients in thyroid dysfunction. (Sudanese journal of paediatrics, 2020) via PubMed

Goji berry

Goji berries are small, dried red berries, also called wolfberries, often eaten as a snack or added to trail mixes and tea. They belong to the nightshade family, so they are set aside during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Gooseberry

Gooseberry is a small, round berry that ranges from tart green to sweeter red, eaten fresh or cooked into sauces, jams, and desserts. It offers vitamin C and fiber, and like most fruit it fits into the reintroduction phase of the Autoimmune Protocol rather than the early elimination phase.

See also: On the food list

Gram-negative bacteria

Gram-negative bacteria are a class of microbes with an outer membrane built from lipopolysaccharide, a molecule that triggers a strong immune response when it is released. This matters to someone healing from autoimmune disease because lipopolysaccharide crossing a weakened gut barrier is one proposed driver of ongoing immune activation.

Reference: Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review. (Internal and emergency medicine, 2023) via PubMed

Graves' disease

Graves' disease is an autoimmune condition in which antibodies stimulate the thyroid gland to release too much hormone, causing an overactive thyroid. It is one of the two major autoimmune thyroid diseases, and recognizing it helps someone understand that thyroid symptoms can be driven by the immune system rather than the thyroid alone.

Reference: Graves disease: latest understanding of pathogenesis and treatment options. (Nature reviews. Endocrinology, 2024) via PubMed

Gravlax

Gravlax is salmon cured rather than cooked, resting in a mixture of salt and seasonings until the flesh turns firm and silky. It is a preparation method rather than an ingredient, and on the Autoimmune Protocol it is made without the sugar and black pepper used in traditional versions.

Green banana flour

Green banana flour is a grain-free flour milled from unripe bananas, with a mild flavor that works in baking and as a thickener. Its main draw is resistant starch, a type of fiber that resists digestion in the small intestine and feeds bacteria further down the gut.

See also: On the food list

Ground cherry

Ground cherry, also called cape gooseberry, is a small sweet-tart fruit wrapped in a papery husk. It belongs to the nightshade family, so anyone avoiding nightshades on the Autoimmune Protocol leaves it out along with tomatoes, peppers, and eggplant.

See also: On the food list

Guava

Guava is a fragrant tropical fruit with sweet flesh in shades of pink or white, eaten fresh, juiced, or cooked into paste. It is a good source of vitamin C and fits into fruit servings once someone has moved into reintroduction.

See also: On the food list

Gums (guar, xanthan, carrageenan)

Gums such as guar, xanthan, and carrageenan are thickeners and stabilizers used in many processed foods, sauces, and dairy alternatives to add body and shelf life. They are avoided on the Autoimmune Protocol because they are associated with gut irritation for some people.

See also: On the food list

Gut barrier (intestinal lining)

The gut barrier is the single-cell-thick wall of the small intestine meant to let digested nutrients through while keeping larger food particles, toxins, and microbes out. A weakened gut barrier is central to the working model of how autoimmune disease may develop and progress.

Reference: Partners in Leaky Gut Syndrome: Intestinal Dysbiosis and Autoimmunity. (Frontiers in immunology, 2021) via PubMed

Gut motility

Gut motility is the coordinated muscle movement that pushes food and waste through the digestive tract at a steady pace. Motility that runs too slow or too fast is tied to different symptom patterns, including bacterial overgrowth and the constipation or diarrhea many people with autoimmune disease experience.

Reference: Gastrointestinal Physiology and Function. (Handbook of experimental pharmacology, 2017) via PubMed

Gut-associated lymphoid tissue (GALT)

Gut-associated lymphoid tissue, or GALT, is the largest concentration of immune tissue in the body, packed into the wall of the intestine. It is where the immune system makes many of its ongoing decisions about which foods and bacteria to tolerate and which to attack, making it a key player in autoimmune disease.

Reference: The Microbiome and Food Allergy. (Annual review of immunology, 2019) via PubMed

Gut-brain axis

The gut-brain axis is the two-way communication network linking the gut, the brain, and the immune system through nerves, hormones, and inflammatory signals. It helps explain why digestive symptoms and mood or stress often rise and fall together in autoimmune disease.

Reference: The Microbiota-Gut-Brain Axis: Psychoneuroimmunological Insights. (Nutrients, 2023) via PubMed

H. pylori

Helicobacter pylori is a bacterium that can colonize the stomach lining and is linked to reduced stomach acid production, poorer absorption of iron and vitamin B12, and ongoing immune activation. Testing for and addressing it is a common early step for someone with autoimmune thyroid disease and unexplained nutrient deficiencies.

Reference: Microorganisms associated to thyroid autoimmunity. (Autoimmunity reviews, 2020) via PubMed

Hashimoto's thyroiditis

Hashimoto's thyroiditis is an autoimmune condition in which the immune system gradually attacks the thyroid gland, and it is the most common cause of an underactive thyroid. It matters to anyone with fatigue, weight changes, or brain fog because a standard thyroid panel often misses it unless thyroid antibodies are specifically tested.

Reference: Hashimoto's thyroiditis: An update on pathogenic mechanisms, diagnostic protocols, therapeutic strategies, and potential malignant transformation. (Autoimmunity reviews, 2020) via PubMed

Heart rate variability

Heart rate variability is the small, natural variation in time between heartbeats, and a higher variability generally reflects a nervous system that can shift smoothly between stress and rest. Tracking it can give someone with autoimmune disease an early signal of overtraining or unmanaged stress before symptoms flare.

Reference: Balancing the autonomic nervous system to reduce inflammation in rheumatoid arthritis. (Journal of internal medicine, 2017) via PubMed

Heavy metals

Heavy metals such as lead, mercury, and cadmium are environmental toxins that can accumulate in the body over time through food, water, and air. Researchers study their possible role in triggering or worsening immune dysregulation, which is why exposure history sometimes comes up in autoimmune disease investigation.

Reference: Mercury-induced inflammation and autoimmunity. (Biochimica et biophysica acta. General subjects, 2019) via PubMed

Hemoglobin

Hemoglobin is the oxygen-carrying protein packed into red blood cells, and it is the standard marker used to check for anemia on a basic blood panel. Low hemoglobin in someone with autoimmune disease can point to nutrient malabsorption, chronic inflammation, or blood loss that is worth investigating.

Reference: Anemia of inflammation. (Blood, 2018) via PubMed

Hemoglobin A1c (HbA1c)

Hemoglobin A1c is a blood test that reflects average blood sugar over roughly the past three months, based on how much sugar has attached to hemoglobin in that time. It is a useful marker for someone with autoimmune disease because blood sugar swings can add to inflammation and make symptoms harder to manage.

Hijiki

Hijiki is a black, stringy sea vegetable with a mild, briny flavor that is soaked before cooking and used in Japanese dishes. It offers minerals such as iron and calcium, though its natural arsenic content means it is eaten in modest amounts rather than daily.

See also: On the food list

Histamine intolerance

Histamine intolerance is a pattern in which the body cannot break down histamine fast enough, so histamine-rich foods such as fermented foods, aged cheese, and leftovers trigger symptoms like headaches, flushing, hives, or digestive upset. It often overlaps with gut dysfunction and can complicate an Autoimmune Protocol elimination if fermented foods are reintroduced too soon.

Reference: Histamine Intolerance-The More We Know the Less We Know. A Review. (Nutrients, 2021) via PubMed

HLA-DQ2 / HLA-DQ8

HLA-DQ2 and HLA-DQ8 are genetic markers that make a person more likely to mount an immune reaction to gluten. Carrying one of these genes is part of the genetic susceptibility piece of the autoimmune model, alongside environmental triggers and gut barrier changes, though carrying the gene does not mean disease is guaranteed.

Reference: The HLA complex and coeliac disease. (International review of cell and molecular biology, 2020) via PubMed

Holy basil

Holy basil, also called tulsi or kaprao, is an aromatic herb with a peppery, clove-like flavor used fresh in Thai cooking and dried as a tea. It is traditionally regarded as an adaptogen, meaning it is studied for a possible role in supporting the body's response to stress.

See also: On the food list

Homocysteine

Homocysteine is an amino acid that can accumulate in the blood when methylation and B vitamin metabolism, particularly folate, B12, and B6, are not working efficiently. Elevated homocysteine is linked to inflammation and cardiovascular and neurological concerns, making it a useful marker to track in autoimmune disease management.

Reference: Hyperhomocysteinemia in Cardiovascular Diseases: Revisiting Observational Studies and Clinical Trials. (Thrombosis and haemostasis, 2022) via PubMed

Horned melon

Horned melon, also called kiwano, is a spiky orange melon with jelly-like green flesh and a mild flavor somewhere between cucumber and lime. It is eaten fresh by scooping out the pulp and works well as fruit once someone has moved past strict elimination.

See also: On the food list

Horseradish

Horseradish is a pungent root that is peeled and grated to make a sharp, spicy condiment. It is compliant on the Autoimmune Protocol as long as it has not been mixed with vinegar-based additives or nightshade spices.

HPA axis (hypothalamic-pituitary-adrenal axis)

The HPA axis, short for hypothalamic-pituitary-adrenal axis, is the communication loop between the brain and the adrenal glands that coordinates the body's stress response and cortisol release. Chronic stress can dysregulate this axis, and that dysregulation is closely tied to the fatigue and immune imbalance common in autoimmune disease.

Reference: Chronic Stress and Autoimmunity: The Role of HPA Axis and Cortisol Dysregulation. (International journal of molecular sciences, 2025) via PubMed

Huckleberry

Huckleberry is a small wild berry similar in appearance to a blueberry, with a more intense, slightly tart flavor. It is eaten fresh, baked, or made into jam, and offers the antioxidants typical of dark berries.

See also: On the food list

Hyperthyroidism

Hyperthyroidism is a state of excess thyroid hormone that speeds up the body's processes, causing a racing heart, anxiety, weight loss, and heat intolerance. In autoimmune disease it is most often caused by Graves' disease, so identifying the underlying immune driver shapes how it is managed.

Reference: Hyperthyroidism: aetiology, pathogenesis, diagnosis, management, complications, and prognosis. (The lancet. Diabetes & endocrinology, 2023) via PubMed

Hypochlorhydria

Hypochlorhydria is a state of low stomach acid that can reduce the breakdown of protein and the absorption of iron and vitamin B12. It is common in autoimmune thyroid disease and can quietly worsen fatigue and nutrient deficiencies if it goes unrecognized.

Reference: Micronutrient deficiencies in patients with chronic atrophic autoimmune gastritis: A review. (World journal of gastroenterology, 2017) via PubMed

Hypocortisolism

Hypocortisolism is a pattern of chronically low cortisol output from the adrenal glands, often following long periods of unmanaged stress. It is linked to persistent fatigue, low stress tolerance, and difficulty getting going in the morning, which many people with autoimmune disease recognize.

Reference: A new view on hypocortisolism. (Psychoneuroendocrinology, 2005) via PubMed

Hypothyroidism

Hypothyroidism is a state in which the thyroid does not produce enough hormone, which slows metabolism and is linked to fatigue, cold sensitivity, weight gain, and constipation. Hashimoto's thyroiditis is the most common autoimmune cause, so a full thyroid antibody panel matters alongside standard thyroid labs.

Reference: Hypothyroidism: A Review. (JAMA, 2025) via PubMed

Immune dysregulation

Immune dysregulation is a loss of the immune system's normal checks and balances, leading to responses that are too strong, misdirected, or aimed at the body's own tissue. It sits at the center of every autoimmune disease and is the process that protocols like the Autoimmune Protocol aim to calm.

Reference: The multiple pathways to autoimmunity. (Nature immunology, 2017) via PubMed

Immune system

The immune system is the body's defense network of cells, tissues, and proteins that recognizes and removes threats such as viruses, bacteria, and damaged cells. In autoimmune disease, this same network mistakenly identifies healthy tissue as a threat and attacks it.

Reference: Overview of the immune response. (The Journal of allergy and clinical immunology, 2010) via PubMed

Immune tolerance

Immune tolerance is the immune system's learned ability to recognize the body's own tissues and harmless substances, such as food, and leave them alone. A breakdown in immune tolerance is one of the defining features of autoimmune disease, whatever tissue ends up being targeted.

Reference: CTLA-4: From mechanism to autoimmune therapy. (International immunopharmacology, 2020) via PubMed

Industrial seed oils

Industrial seed oils are highly processed oils extracted from seeds and grains, including canola, corn, soybean, sunflower, safflower, cottonseed, and grapeseed. They are avoided on the Autoimmune Protocol because their high omega-6 content and processing methods are thought to tilt the body toward inflammation.

Inflammation

Inflammation is the immune system's response to injury, infection, or irritation, and it is useful in short, targeted bursts to help the body heal. It becomes a problem when it runs low-grade and constant, which is the pattern seen across autoimmune disease and many chronic conditions.

Reference: Low-Grade Chronic Inflammation: a Shared Mechanism for Chronic Diseases. (Physiology (Bethesda, Md.), 2024) via PubMed

Inflammatory bowel disease (IBD)

Inflammatory bowel disease is a group of conditions, mainly Crohn's disease and ulcerative colitis, involving chronic immune-driven inflammation of the digestive tract. It is distinct from irritable bowel syndrome, and someone with IBD often benefits from the same gut-focused, food-based approach used across autoimmune disease.

Reference: A Comprehensive Review and Update on the Pathogenesis of Inflammatory Bowel Disease. (Journal of immunology research, 2019) via PubMed

Inflammatory markers

Inflammatory markers are blood tests, such as C-reactive protein and erythrocyte sedimentation rate, used to estimate how much inflammation is present in the body at a given time. Tracking them over time can help someone with autoimmune disease see whether dietary and lifestyle changes are having an effect.

Reference: Erythrocyte Sedimentation Rate and C-reactive Protein Measurements and Their Relevance in Clinical Medicine. (WMJ : official publication of the State Medical Society of Wisconsin, 2016) via PubMed

Innate immunity

Innate immunity is the fast, general arm of the immune system that responds to threats immediately, using physical barriers and cells such as macrophages and natural killer cells rather than a targeted, learned response. It works alongside adaptive immunity, and imbalance between the two is part of the picture in autoimmune disease.

Reference: Control of adaptive immunity by pattern recognition receptors. (Immunity, 2024) via PubMed

Instant Pot

An Instant Pot is a brand of electric multi-cooker that pressure-cooks food quickly, cutting the time needed to make broths, stews, and braises. Autoimmune Protocol recipes often call for one to turn tougher cuts of meat and bone broth around in far less time than the stovetop.

Insulin resistance

Insulin resistance is a state in which cells respond less to insulin, so the pancreas produces more of it to keep blood sugar in a normal range. It is linked to inflammation and hormonal imbalance, and it shows up more often alongside autoimmune disease than in the general population.

Reference: Insulin Resistance: From Mechanisms to Therapeutic Strategies. (Diabetes & metabolism journal, 2021) via PubMed

Intestinal permeability ('leaky gut')

Intestinal permeability describes a gut barrier that is more open than it should be, allowing food particles, toxins, and microbes to cross into the tissue beneath and reach the immune system. It is a proposed contributing mechanism in autoimmune disease, not a stand-alone diagnosis, and it is one reason gut healing is central to the Autoimmune Protocol.

Reference: Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review. (Internal and emergency medicine, 2023) via PubMed

Intrinsic factor

Intrinsic factor is a protein made by cells in the stomach lining that is required to absorb vitamin B12 from food further down in the small intestine. Autoimmune attack on these stomach cells, known as pernicious anemia, can cause B12 deficiency even when someone eats plenty of B12-rich food.

Reference: Autoimmune Gastritis. (Archives of pathology & laboratory medicine, 2019) via PubMed

Inulin

Inulin is a prebiotic fiber found in chicory root, Jerusalem artichoke, and coconut that passes through the small intestine undigested and feeds bacteria in the colon. It supports a diverse gut microbiome, though eating too much at once commonly causes gas and bloating.

See also: On the food list

Iodine

Iodine is a mineral the thyroid gland uses as a building block for its hormones. Both too little and too much iodine are linked to thyroid problems, so intake is approached carefully in autoimmune thyroid disease rather than assumed to be simply more is better.

Reference: Multiple nutritional factors and thyroid disease, with particular reference to autoimmune thyroid disease. (The Proceedings of the Nutrition Society, 2018) via PubMed

Ivy gourd

Ivy gourd, also called tindora or kundru, is a small green gourd with a mild, slightly crisp texture, commonly stir-fried or curried in South Asian cooking. It is prepared much like a young zucchini once it is cut open and cooked.

See also: On the food list

Jabuticaba

Jabuticaba is a grape-like Brazilian fruit with thick purple-black skin and sweet, juicy flesh that grows in clusters directly on the tree trunk. It is eaten fresh or made into jams, jellies, and wine.

See also: On the food list

Jackfruit

Jackfruit is a very large tropical fruit whose sweet, ripe flesh is eaten as fruit, while the fibrous, unripe flesh is cooked and used as a savory, meat-like ingredient in stews and tacos. Unripe jackfruit is prized on the Autoimmune Protocol for its texture in place of shredded meat.

See also: On the food list

Java plum

Java plum, also called jamun or black plum, is a small, dark purple tropical fruit with a sweet-tart, slightly astringent taste. It is eaten fresh with the seed removed, and traditional use has long connected it to blood sugar balance, separate from its role as an everyday fruit.

See also: On the food list

Jerusalem artichoke

Jerusalem artichoke, also called sunchoke, is a knobby root vegetable with a sweet, nutty flavor, roasted, mashed, or eaten raw and thinly sliced. It is high in inulin, a fiber that can cause gas for people whose gut bacteria are not yet used to it.

See also: On the food list

Jicama

Jicama is a round, crisp root vegetable with a mild, slightly sweet flavor, usually peeled to remove the tough brown skin before eating. It is eaten raw for crunch in place of crackers or chips, or cooked into stir-fries.

See also: On the food list

Job's tears

Job's tears is a large, chewy grain with a texture similar to barley, used in soups, porridges, and teas across Asian cooking. Like other grains, it falls outside the elimination phase of the Autoimmune Protocol, which removes all grains regardless of whether they contain gluten.

See also: On the food list

Jujube

Jujube, also called Chinese date or ber, is a small fruit eaten fresh when it is crisp and apple-like, or dried when it turns sweet, chewy, and date-like. Dried jujube is used in teas and broths in Chinese cooking as well as eaten on its own.

See also: On the food list

Julienne

Julienne is a knife cut that turns vegetables or other food into thin, matchstick-sized strips of even width. It is used when a recipe calls for pieces that cook quickly and evenly or that add texture to a salad or stir-fry.

Juniper

Juniper is a small, dark berry with a piney, resinous flavor, most often used whole or crushed to season game meats, brines, and slow-cooked dishes. A few berries go a long way, since the flavor is strong.

See also: On the food list

Kabocha squash

Kabocha squash, also called Japanese pumpkin, is a round, dark green winter squash with dense, sweet, dry flesh similar to a cross between pumpkin and sweet potato. The skin is edible once roasted, so it needs less peeling than many other winter squash.

See also: On the food list

Kaffir lime

Kaffir lime, also called makrut lime, is a bumpy citrus whose fragrant leaves and zest flavor Southeast Asian soups and curries far more than its small amount of juice. The leaves are usually simmered whole and removed before serving, similar to a bay leaf.

See also: On the food list

Kamut

Kamut, also called khorasan wheat, is an ancient variety of wheat with a larger kernel and a slightly buttery flavor. It still contains gluten, so it is excluded on the Autoimmune Protocol and by anyone avoiding gluten.

See also: On the food list

Kefir

Kefir is a tangy, drinkable fermented milk rich in probiotics, made by fermenting milk with a culture of bacteria and yeast. A non-dairy version can be made the same way using coconut milk, which fits the Autoimmune Protocol where dairy kefir does not.

Key lime

Key lime is a small, very tart, and aromatic lime, more fragrant and acidic than the common Persian lime found in most grocery stores. It is used for its juice and zest in cooking and baking.

See also: On the food list

Kohlrabi

Kohlrabi is a round, pale green or purple vegetable in the cabbage family with a crisp texture and a mild flavor similar to a sweet broccoli stem. It can be eaten raw, sliced thin for salads, or cooked like a turnip.

See also: On the food list

Kokum

Kokum is a dried, dark, sour fruit rind from India, used to add tang and a deep reddish color to curries, chutneys, and cooling drinks. It works similarly to tamarind as a souring agent in cooking.

See also: On the food list

Komatsuna

Komatsuna, also called Japanese mustard spinach, is a mild leafy green that can be eaten raw when young or cooked briefly like spinach. It holds up well in stir-fries and soups without turning bitter.

See also: On the food list

Kombu

Kombu is a thick, dark sea vegetable used to add savory depth to broths and to help soften beans and other foods as they cook. It is usually removed before serving and is naturally high in iodine, so it is used in modest amounts, especially for autoimmune thyroid disease.

See also: On the food list

Kombucha

Kombucha is a lightly fizzy, tangy fermented tea made by fermenting sweetened tea with a culture of bacteria and yeast. It is valued as a source of probiotics, though the natural caffeine and residual sugar are worth factoring in for anyone sensitive to either.

See also: On the food list

Kumquat

Kumquat is a tiny oval citrus fruit eaten whole, peel and all, with a sweet rind and tart, juicy flesh. It is eaten fresh, candied, or made into marmalade.

See also: On the food list

Kuzu

Kuzu is a fine white starch made from the root of the kudzu plant, used to thicken sauces, soups, and puddings much the way arrowroot or cornstarch would be. It is dissolved in a small amount of cold liquid before being stirred into a hot dish so it thickens without clumping.

Kvass

Kvass is a tangy, lightly fermented drink traditionally made from beets or stale bread, often flavored with ginger or herbs. Beet kvass is the version most used on the Autoimmune Protocol, valued as a source of probiotics.

See also: On the food list

L-glutamine

L-glutamine is an amino acid that serves as the main fuel source for the cells lining the small intestine, supporting their repair and turnover. It is studied for a possible role in supporting the gut barrier, which is why it shows up often in gut-healing approaches for autoimmune disease.

Reference: Glutamine and the regulation of intestinal permeability: from bench to bedside. (Current opinion in clinical nutrition and metabolic care, 2017) via PubMed

Lacto-fermented

Lacto-fermented describes food preserved by beneficial bacteria that convert natural sugars into lactic acid, the traditional method behind sauerkraut, pickles, and some yogurts. The process gives the food a tangy flavor and a naturally higher probiotic content than food preserved with vinegar.

Lactulose breath test

A lactulose breath test measures hydrogen and methane gas after someone drinks a non-digestible sugar, used to check for bacterial overgrowth in the small intestine. It is a common diagnostic step when bloating, gas, or irregular digestion point toward small intestinal bacterial overgrowth rather than food sensitivity alone.

Reference: Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. (The American journal of gastroenterology, 2017) via PubMed

Ladoo

Ladoo is a round Indian sweet traditionally made from flour, sugar, and ghee, adapted here into a grain-free version using ingredients like tigernut flour and coconut. It is rolled into small balls by hand and eaten as a treat.

See also: On the food list

Lard

Lard is rendered pork fat, prized in cooking and baking for its neutral flavor and stability at high heat. It is a compliant fat on the Autoimmune Protocol as long as it comes from pasture-raised pork without additives.

Latency

Latency describes a virus settling into the body in a dormant, non-active state instead of being cleared entirely. It can reactivate later under stress or immune changes. For someone healing from autoimmune disease, some latent viruses, such as Epstein-Barr, are studied as possible triggers for immune flares.

Reference: EBV Latency Programs: Molecular and Epigenetic Regulation and Its Role in Disease Pathogenesis. (Journal of medical virology, 2025) via PubMed

Leaf lard

Leaf lard is the mildest and purest pork fat, rendered from the fat around the kidneys. Its light, neutral flavor makes it a favorite for baking and frying on the Autoimmune Protocol, where butter and most seed oils are off the table.

See also: On the food list

Leaky brain

Leaky brain describes increased permeability of the blood brain barrier, the lining that normally keeps the brain separate from circulating immune cells and toxins. It is discussed alongside leaky gut, since inflammation crossing a compromised gut lining may also affect the brain. This connection helps explain brain fog and mood changes during autoimmune flares.

Reference: Blood-Brain Barrier Disruption in Neuroimmunological Disease. (International journal of molecular sciences, 2024) via PubMed

Lectins

Lectins are proteins found in plants, concentrated in legumes and grains, that bind to sugars on the surface of cells lining the gut. In sensitive people this binding can irritate the gut lining and contribute to increased permeability. This is one reason legumes and grains are removed during the elimination phase of the Autoimmune Protocol.

Reference: The dietary intake of wheat and other cereal grains and their role in inflammation. (Nutrients, 2013) via PubMed

Legume

Legume is the plant family Fabaceae, which includes beans, lentils, peanuts, soy, and peas, along with less obvious members like tamarind, fenugreek, jicama, carob, and rooibos. All legumes are removed during the elimination phase of the Autoimmune Protocol because of their lectin and protein content.

See also: On the food list

Lemon balm

Lemon balm is a lemon-scented herb in the mint family, also called melissa. Its fresh or dried leaves flavor teas and add brightness to dressings and cooked dishes, and it is a calming herb many people enjoy in the evening.

Lemon verbena

Lemon verbena is a fragrant herb with a strong, clean lemon scent and flavor. Its leaves are steeped for tea or used to flavor desserts, dressings, and infused waters, and it is a pleasant substitute for citrus zest when a recipe calls for bright lemon flavor without the fruit itself.

See also: On the food list

Lemongrass

Lemongrass is a tall, fibrous grass with a bright, citrusy flavor common in Southeast Asian cooking. The tough outer stalk is bruised, sliced thin, or finely minced to release its aroma into soups, marinades, and curries, then often removed before serving.

See also: On the food list

Levothyroxine

Levothyroxine is a common thyroid medication that supplies synthetic T4, the storage form of thyroid hormone, and relies on the body to convert it into active T3. It is sold under several brand and generic names. Many people managing Hashimoto's or hypothyroidism take it, though some find they also need a T3-containing medication to feel well.

Reference: Personalized Approaches to Hypothyroidism: The Role of Triiodothyronine (T3) in Thyroid Hormone Replacement. (Cureus, 2025) via PubMed

LH (luteinizing hormone)

Luteinizing hormone, or LH, is released by the pituitary gland and triggers ovulation in women, while supporting testosterone production in men. Tracking its pattern alongside other hormones can help identify cycle irregularities that are common when autoimmune disease and chronic inflammation disrupt the hormone system.

Reference: Thyroid dysfunction and thyroid autoimmunity in euthyroid women in achieving fertility. (European review for medical and pharmacological sciences, 2015) via PubMed

Lingonberry

Lingonberry is a small, tart red berry common in Scandinavian cooking, related to blueberries and cranberries. It is usually simmered into a sauce or jam and served alongside savory dishes rather than eaten on its own.

See also: On the food list

Liothyronine

Liothyronine is a thyroid medication that supplies active T3 directly, rather than relying on the body to convert it from T4. It acts quickly and is typically prescribed alongside a T4 medication, under a prescriber's guidance, for people whose conversion of T4 to T3 is impaired.

Reference: Guidelines for the treatment of hypothyroidism: prepared by the american thyroid association task force on thyroid hormone replacement. (Thyroid : official journal of the American Thyroid Association, 2014) via PubMed

Lipopolysaccharide (LPS)

Lipopolysaccharide, or LPS, is a component of the outer wall of certain gut bacteria. When it crosses a compromised gut lining into the bloodstream, it strongly activates the immune system and drives inflammation throughout the body. Rising LPS is one reason gut healing is central to managing autoimmune disease.

Reference: Role of Metabolic Endotoxemia in Systemic Inflammation and Potential Interventions. (Frontiers in immunology, 2021) via PubMed

Loganberry

Loganberry is a dark red berry, a natural cross between a raspberry and a blackberry, with a tart, juicy flavor. It is eaten fresh when in season and also made into jams, syrups, and baked goods.

See also: On the food list

Longan

Longan is a small, round tropical fruit, also called dragon eye for the dark seed visible through its translucent flesh. Its flavor is sweet and slightly musky, similar to lychee, and it is eaten fresh or dried.

See also: On the food list

Loquat

Loquat is a small orange tropical fruit with juicy, sweet-tart flesh and a few large seeds. It is eaten fresh out of hand or cooked down into jams and preserves.

See also: On the food list

Lotus root

Lotus root is the crunchy, mild-flavored root of the lotus plant, recognizable by the lacy pattern of holes revealed when it is sliced. It is stir-fried, braised, or added to soups for texture, and holds its crunch well through cooking.

Lovage

Lovage is a leafy herb with a strong flavor similar to celery, though more intense. Its leaves and stems season soups, stocks, and salads, and a small amount goes a long way.

See also: On the food list

Lupus (SLE)

Lupus, fully called systemic lupus erythematosus or SLE, is an autoimmune condition in which the immune system produces antibodies that attack healthy tissue throughout the body, including skin, joints, kidneys, and other organs. Symptoms vary widely between people and can flare and settle over time, which makes diet and lifestyle management an important part of care.

Reference: Novel paradigms in systemic lupus erythematosus. (Lancet (London, England), 2019) via PubMed

Luteal phase

The luteal phase is the second half of the menstrual cycle, beginning after ovulation, when progesterone rises to prepare the uterine lining. Its length and the level of progesterone reached are often used to gauge cycle health, and both can shift when autoimmune disease and chronic stress affect the hormone system.

Lychee

Lychee is a small tropical fruit with a rough, bright red shell that peels away from sweet, fragrant white flesh surrounding a single seed. It is usually eaten fresh, though it can also be found dried or canned.

See also: On the food list

Mace

Mace is a warm, aromatic spice made from the lacy covering that surrounds the nutmeg seed. Its flavor is close to nutmeg but lighter and more delicate, and it is used in both sweet and savory dishes.

Mache

Mache, also called lamb's lettuce, is a small, tender salad green with a soft texture and a mild, nutty flavor. Its delicate leaves are usually served whole in salads rather than chopped.

See also: On the food list

Macrophage

A macrophage is an immune cell that engulfs and clears pathogens, damaged cells, and cellular debris. It also releases signals that call other immune cells into action, making it a key player in both fighting infection and driving the chronic inflammation seen in autoimmune disease.

Reference: Macrophage polarization: an important role in inflammatory diseases. (Frontiers in immunology, 2024) via PubMed

Magnesium

Magnesium is a mineral involved in hundreds of processes in the body, including muscle relaxation, nerve signaling, sleep, and blood sugar regulation. Many people run low on it, and inadequate magnesium has been linked to worsened inflammation and fatigue, which makes it a common focus in autoimmune healing.

Reference: Magnesium: Health Effects, Deficiency Burden, and Future Public Health Directions. (Nutrients, 2025) via PubMed

Malabar spinach

Malabar spinach, also called basella or pui, is a leafy vine grown in warm climates. Its thick, slightly mucilaginous leaves are cooked much like true spinach, in soups, stir-fries, and stews.

See also: On the food list

Malanga

Malanga, also called yautia or cocoyam, is a starchy tropical root used much like potato or taro. It has a rough, hairy skin and must always be peeled and fully cooked before eating.

See also: On the food list

Mamey sapote

Mamey sapote is a tropical fruit with rough brown skin and soft, sweet, orange-red flesh. Its flavor is often compared to a blend of sweet potato and pumpkin, and it is eaten fresh, blended into drinks, or used in desserts.

See also: On the food list

Mandoline

A mandoline is a kitchen tool with a fixed, very sharp blade that slices vegetables and fruit into thin, even pieces quickly. It saves time on dishes that call for uniform slices, and its blade is sharp enough that using the hand guard matters.

Mangosteen

Mangosteen is a tropical fruit with a thick, deep purple rind that opens to reveal sweet, juicy white segments inside. Its flavor is often described as a mix of peach and citrus.

See also: On the food list

Maple sugar

Maple sugar is a granulated sweetener made by boiling maple syrup until nearly all the water evaporates. It has the same rich, caramel-like flavor as maple syrup and is used in moderation on the Autoimmune Protocol.

See also: On the food list

Marinate

To marinate is to soak food, usually meat, poultry, or vegetables, in a seasoned liquid before cooking. The process adds flavor and can help tenderize tougher cuts, depending on how long the food sits and what the marinade contains.

Marjoram

Marjoram is a mild, sweet herb closely related to oregano, though gentler in flavor. It is used fresh or dried in soups, sauces, and meat dishes, often added near the end of cooking to preserve its delicate taste.

Mast cell

A mast cell is an immune cell found throughout body tissues, especially near the skin, gut, and airways. When triggered, it releases histamine and other chemicals that drive allergic and inflammatory reactions, which makes it relevant to symptoms like flushing, hives, and digestive upset in sensitive people.

Reference: Mast Cell Biology at Molecular Level: a Comprehensive Review. (Clinical reviews in allergy & immunology, 2020) via PubMed

Mast cell activation

Mast cell activation describes a pattern where mast cells release histamine and other chemicals more readily or more often than they should, sometimes without an obvious trigger. It is linked to symptoms like flushing, itching, hives, and digestive upset, and it can complicate autoimmune healing when foods or stress set off reactions unpredictably.

Reference: Mast cell activation syndrome: Current understanding and research needs. (The Journal of allergy and clinical immunology, 2024) via PubMed

Matcha

Matcha is a bright green Japanese tea made by grinding whole tea leaves into a fine powder, then whisking the powder into hot water or milk rather than steeping and removing leaves. Because the whole leaf is consumed, it carries more caffeine than a typical steeped tea.

See also: On the food list

Medlar

Medlar is a small brown fruit that is only eaten once it has softened well past ripeness, a process called bletting. Its flavor is often compared to spiced applesauce, and it belongs to the same family as apples and pears.

See also: On the food list

Melatonin

Melatonin is a hormone released as darkness falls, helping signal to the body that it is time to sleep. Light exposure at night, especially blue light from screens, can suppress its release, and disrupted melatonin is linked to the poor sleep that often worsens autoimmune symptoms.

Reference: Melatonin supplementation improves rheumatological disease activity: A systematic review. (Clinical nutrition ESPEN, 2023) via PubMed

Melon pear

Melon pear, also called pepino dulce, is a small fruit with pale yellow-green skin and mildly sweet, juicy flesh. Its flavor sits somewhere between melon and cucumber, and it is eaten fresh, chilled, or added to fruit salads.

See also: On the food list

Menopause

Menopause is defined as twelve months without a menstrual period, marking the point when the ovaries have stopped releasing eggs and monthly cycles have ended. The hormone shifts around menopause can intersect with autoimmune disease, sometimes changing symptom patterns that were established for years.

Reference: The Impact of Menopause on Autoimmune and Rheumatic Diseases. (Clinical reviews in allergy & immunology, 2025) via PubMed

Methylation

Methylation is a cellular process that attaches a small chemical tag, called a methyl group, onto DNA, hormones, and other molecules. It supports detoxification, gene regulation, and how the body uses nutrients like folate and B12, and differences in methylation capacity are often discussed in autoimmune and chronic illness care.

Reference: MTHFR-folate axis as a modulator of the epigenetic landscape in autoimmune diseases (Review). (International journal of molecular medicine, 2026) via PubMed

Methylcobalamin

Methylcobalamin is an active form of vitamin B12 that cells can use directly, without needing to convert it first. It is sometimes preferred in supplements for people whose bodies process standard B12 or folate less efficiently, though most people absorb either form well.

Reference: Vitamin B12: A Comprehensive Review of Natural vs Synthetic Forms of Consumption and Supplementation. (Cureus, 2025) via PubMed

Methylfolate

Methylfolate is the active, ready-to-use form of folate, the B vitamin needed for cell division and DNA repair. People with certain MTHFR gene variants convert the standard form, folic acid, into this active form less efficiently, so some supplements provide methylfolate directly.

Reference: Folate, folic acid and 5-methyltetrahydrofolate are not the same thing. (Xenobiotica; the fate of foreign compounds in biological systems, 2014) via PubMed

Methylmalonic acid (MMA)

Methylmalonic acid, or MMA, is a marker that rises in the blood or urine when cells are not able to use vitamin B12 effectively. It can reveal a functional B12 shortage even when a standard blood B12 test looks normal, which matters for anyone dealing with fatigue or nerve symptoms.

Reference: Vitamin B12-Related Biomarkers. (Food and nutrition bulletin, 2024) via PubMed

Meyer lemon

Meyer lemon is a cross between a lemon and an orange, giving it a sweeter, less acidic flavor than a standard lemon. Its skin is thin and fragrant, and the whole fruit, zest included, is often used in cooking and baking.

See also: On the food list

Microbiome

The microbiome is the vast community of bacteria, fungi, and other microorganisms living mainly in the gut. It influences digestion, immune function, and the production of certain neurotransmitters, and its balance is considered central to healing in autoimmune disease.

Reference: Gut Microbiota, Leaky Gut, and Autoimmune Diseases. (Frontiers in immunology, 2022) via PubMed

Migrating motor complex

The migrating motor complex is a wave of cleansing muscle activity that sweeps through the small intestine between meals, moving leftover food particles and bacteria along. Weak or infrequent waves are linked to small intestinal bacterial overgrowth, which is one reason spacing meals with time to fast in between matters for gut health.

Reference: The migrating motor complex: control mechanisms and its role in health and disease. (Nature reviews. Gastroenterology & hepatology, 2012) via PubMed

Miso

Miso is a savory, salty paste made from fermented soybeans, sometimes combined with rice or barley. It is stirred into soups and sauces near the end of cooking to preserve its live cultures and deep, umami flavor.

Mitsuba

Mitsuba, also called Japanese parsley or trefoil, is a delicate herb with a fresh, mild flavor somewhere between parsley and celery. It is added to soups, salads, and simmered dishes, usually near the end of cooking.

See also: On the food list

Mizuna

Mizuna is a feathery Japanese salad green with a mild, peppery bite. It can be eaten raw in salads or lightly cooked into stir-fries and soups, where its texture softens but its flavor holds.

See also: On the food list

Moderation (in this database)

In this database, moderation marks a Core food that is eaten in smaller amounts because it is starchy or naturally sweet, such as grain-free flours, honey, and maple syrup. These foods are technically allowed on the Autoimmune Protocol and are best kept occasional rather than a daily staple.

Modified AIP

Modified AIP, meaning a modified Autoimmune Protocol, is a gentler starting point that allows some less-reactive foods, such as egg yolk, seeds, and edible-pod legumes, from the beginning instead of waiting for reintroduction. In this database those foods are listed under Reintroduction rather than Core.

Molasses

Molasses is a thick, dark syrup left behind after sugar is refined from sugarcane or beets. Its flavor is deep and slightly bitter, and it is used in small amounts on the Autoimmune Protocol as an occasional sweetener.

See also: On the food list

Mold (in the body)

Mold, in this context, refers to exposure to mold and the toxins it produces, often from water-damaged buildings and sometimes from certain foods. In sensitive people, ongoing mold exposure can keep the immune system activated, which is why some autoimmune protocols include checking the home environment alongside diet.

Reference: Mold, Mycotoxins and a Dysregulated Immune System: A Combination of Concern? (International journal of molecular sciences, 2021) via PubMed

Molecular mimicry

Molecular mimicry happens when a food protein is shaped closely enough like one of the body's own tissues that an immune response built against the food starts mistaking that tissue for the intruder. It is the leading proposed mechanism behind the link between gluten and thyroid autoimmunity.

Reference: Molecular mimicry and autoimmunity. (Journal of autoimmunity, 2018) via PubMed

Morel

Morel is a wild mushroom with a distinctive honeycombed cap and a rich, earthy, nutty flavor. It must always be cooked thoroughly before eating and is never served raw, since raw morels contain compounds that can cause digestive upset.

See also: On the food list

Moringa leaves

Moringa leaves, also called drumstick leaves or malunggay, are the small green leaves of the moringa tree. They are added to soups and stews and are valued as a source of vitamins and minerals.

See also: On the food list

MTHFR

MTHFR is a gene that codes for an enzyme used in methylation and folate processing. Common variants of this gene are linked to a reduced ability to activate folate into its usable form, which can affect detoxification and how the body handles inflammation over time.

Reference: MTHFR Gene Polymorphisms: A Single Gene with Wide-Ranging Clinical Implications-A Review. (Genes, 2025) via PubMed

Multiple sclerosis

Multiple sclerosis is an autoimmune condition in which the immune system attacks myelin, the protective coating around nerve fibers in the brain and spinal cord. This disrupts communication between nerves and the rest of the body, leading to symptoms that can include numbness, fatigue, and problems with movement or vision.

Reference: Multiple sclerosis pathophysiology: a comprehensive review of genetic, environmental, and immunological drivers. (Inflammopharmacology, 2025) via PubMed

Muscadine

Muscadine is a large, thick-skinned grape native to the southeastern United States, with a musky sweetness distinct from table grapes. It is eaten fresh, seeds and all or spit out, and made into juice, jam, and wine.

See also: On the food list

Mycotoxin

A mycotoxin is a toxic compound produced by certain molds, which can end up in water-damaged buildings or in some stored foods like grains and coffee. Breathing in or eating mycotoxins over time can place ongoing stress on the immune system, which is relevant for anyone managing autoimmune disease.

Reference: Mold and Mycotoxin Exposure and Brain Disorders. (Journal of integrative neuroscience, 2023) via PubMed

Napa cabbage

Napa cabbage is a pale, crinkly-leafed Chinese cabbage with a mild, slightly sweet flavor and a more tender texture than green cabbage. It is used raw in slaws, cooked into stir-fries and soups, or fermented.

See also: On the food list

Naranjilla

Naranjilla is a tart, orange-skinned tropical fruit with green, juicy flesh, popular in juices across South America. It belongs to the nightshade family, so it is left out during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Natto

Natto is a sticky, strong-smelling fermented soybean food from Japan, known for its distinctive texture and pungent flavor. It is typically eaten over rice with a bit of soy sauce or mustard.

See also: On the food list

Natural desiccated thyroid (NDT)

Natural desiccated thyroid, or NDT, is a thyroid medication made from dried pig thyroid glands, containing both T4 and T3 in roughly the same ratio the human thyroid produces. Armour Thyroid is a well-known brand, and some people managing Hashimoto's find it works better for them than synthetic T4 alone.

Reference: Evaluating the effectiveness of combined T4 and T3 therapy or desiccated thyroid versus T4 monotherapy in hypothyroidism: a systematic review and meta-analysis. (BMC endocrine disorders, 2024) via PubMed

Natural killer cell

A natural killer cell is an immune cell that can identify and destroy virus-infected or abnormal cells quickly, without needing prior exposure to the specific threat. This makes it part of the body's fast-response immune defense, distinct from the slower antibody-based response that takes days to develop.

Reference: Human natural killer cells: Form, function, and development. (The Journal of allergy and clinical immunology, 2022) via PubMed

Neuroinflammation

Neuroinflammation is inflammation occurring in the brain and nervous system, which can arise from immune signals traveling from the body or from substances like bacterial toxins reaching the brain. It is increasingly studied as a contributor to the brain fog, mood changes, and fatigue common in autoimmune disease.

Reference: Inflammation From Peripheral Organs to the Brain: How Does Systemic Inflammation Cause Neuroinflammation? (Frontiers in aging neuroscience, 2022) via PubMed

Neurotransmitter

A neurotransmitter is a chemical messenger that nerve cells use to communicate with each other, affecting mood, cognition, and many body functions. Some neurotransmitters, including a large share of the body's serotonin, are made with help from gut bacteria, linking gut health directly to mental and emotional well-being.

Reference: Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. (Behavioural brain research, 2014) via PubMed

NF-kB pathway

The NF-kB pathway is a central signaling system inside cells that switches on many of the genes responsible for inflammation once it is activated by an immune trigger. It plays a role in both normal immune defense and the chronic, low-grade inflammation seen in autoimmune disease.

Reference: NF-κB in biology and targeted therapy: new insights and translational implications. (Signal transduction and targeted therapy, 2024) via PubMed

Nightshade

Nightshade refers to the plant family Solanaceae, which includes tomato, potato, pepper, and eggplant, along with goji berries, the spices made from peppers, and non-food plants like tobacco and ashwagandha. All nightshades are removed during the elimination phase of the Autoimmune Protocol.

Nitric oxide

Nitric oxide is a short-lived signaling molecule with several jobs in the body, including relaxing blood vessels and supporting nerve communication. In one of its forms, it also participates directly in immune attacks on pathogens, so it sits at the crossroads of circulation, nerve function, and immune defense.

Reference: Inducible nitric oxide synthase: Regulation, structure, and inhibition. (Medicinal research reviews, 2019) via PubMed

Nomato

Nomato, a blend of 'no' and 'tomato,' is a sauce made without any nightshades that still delivers the color and tang of a traditional tomato sauce. It is built from cooked vegetables like carrot, beet, and squash, sometimes with a splash of vinegar, so it fits the elimination phase of the Autoimmune Protocol.

Nonnutritive sweetener

A nonnutritive sweetener is a sweetener that provides little or no calories, including aspartame, sucralose, saccharin, stevia, and sugar alcohols. All of these are kept out during the elimination phase of the Autoimmune Protocol, since even calorie-free sweeteners can affect the gut microbiome and blood sugar response.

See also: On the food list

Nopal

Nopal is the flat pad of the prickly pear cactus, sometimes called a cactus paddle. The spines are cut away and the pad is grilled, boiled, or sauteed, with a flavor and texture close to green beans or okra. It is a traditional vegetable in Mexican cooking and fits easily into an Autoimmune Protocol vegetable rotation.

See also: On the food list

Nori

Nori is a thin, dried sheet of sea vegetable, most familiar as the wrap around sushi rolls. It can also be toasted and crumbled over rice, vegetables, or eggs as a savory, mineral-rich seasoning. Sea vegetables like nori are a useful source of iodine for those following the Autoimmune Protocol.

See also: On the food list

NSAIDs

NSAIDs, or nonsteroidal anti-inflammatory drugs, are common over the counter and prescription pain and fever relievers, including ibuprofen and naproxen. Regular use can irritate and increase the permeability of the gut lining, which matters for anyone working to calm gut inflammation as part of autoimmune healing.

Reference: Drug-Induced Small Bowel Injury: a Challenging and Often Forgotten Clinical Condition. (Current gastroenterology reports, 2019) via PubMed

Nutrient density

Nutrient density describes how much vitamin, mineral, and other nourishment a food delivers relative to its size or calories. Foods such as organ meats, seafood, and leafy greens are considered nutrient dense, and building meals around them is a central strategy for rebuilding a well nourished body during autoimmune recovery.

Nutrient-dense (in this database)

This label marks a food in the glossary as a standout source of nourishment within the nutrient-density teaching used throughout this Autoimmune Protocol reference, foods such as liver, oysters, sardines, and dark leafy greens. It is a way to flag priority foods worth returning to often.

Nutritional yeast

Nutritional yeast is deactivated yeast sold as flakes or powder, prized for a savory, cheese-like flavor that works well sprinkled over vegetables or blended into sauces. For the Autoimmune Protocol, choose an unfortified version, since fortified brands often add synthetic vitamins in ways that do not fit the protocol.

See also: On the food list

Occludin

Occludin is a protein that helps form the tight junctions sealing the cells lining the gut wall together. When occludin breaks down, the gut barrier can become more permeable, a state often described as leaky gut, which is one of the mechanisms researchers link to autoimmune disease activity.

Reference: Enterocytes' tight junctions: From molecules to diseases. (World journal of gastrointestinal pathophysiology, 2011) via PubMed

Offal

Offal refers to the organ meats of an animal, including liver, heart, kidney, and tongue. These cuts are among the most nutrient-dense foods available, rich in B vitamins, iron, and other nutrients that are easy to fall short on, and are emphasized throughout the Autoimmune Protocol.

Okra

Okra is a green seed pod eaten as a vegetable, common in Southern and West African cooking. It releases a natural thickening quality as it cooks, which makes it a favorite for stews and gumbo, and it has a mild, slightly grassy flavor on its own.

See also: On the food list

Omega-3 fats

Omega-3 fats are a family of fats found in oily fish such as salmon, sardines, and mackerel, as well as in smaller amounts in some plant foods. They are associated with a calmer inflammatory response in the body, which is one reason fatty fish appears often on Autoimmune Protocol meal plans.

See also: How AIP works on the gut

Optimal range (functional range)

An optimal or functional range is a narrower target that some functional medicine practitioners use when reading lab results, often associated with feeling well rather than simply avoiding disease. It sits inside the wider conventional reference range and can flag an early imbalance before a value would be labeled abnormal.

Oral tolerance

Oral tolerance is the immune system's normal ability to encounter a food in the gut without mounting a reactive immune response against it. Rebuilding oral tolerance to foods that were removed is part of the goal of a slow, careful reintroduction process after time on the Autoimmune Protocol.

Reference: Gut immune system and oral tolerance. (The British journal of nutrition, 2013) via PubMed

Orangelo

An orangelo is a citrus fruit that is a natural cross between an orange and a grapefruit, with juicy, sweet-tart flesh. It can be eaten out of hand or juiced like other citrus fruits allowed on the Autoimmune Protocol.

See also: On the food list

Oregon grape

Oregon grape is a tart, blue-purple berry from a shrub native to the Pacific Northwest, not a true grape. It is more often cooked down into jelly than eaten fresh, since raw berries are quite sour and the seeds are bitter.

See also: On the food list

Ovulation

Ovulation is the release of a mature egg from the ovary, marking the shift from the follicular phase of the menstrual cycle into the luteal phase. Whether and how regularly ovulation occurs is a useful marker of hormonal balance, since autoimmune disease and chronic inflammation can disrupt the cycle.

Reference: Minerals and the Menstrual Cycle: Impacts on Ovulation and Endometrial Health. (Nutrients, 2024) via PubMed

Oxalates

Oxalates are naturally occurring compounds found in some plant foods, including spinach, chard, and taro leaves, that can bind minerals and, in sensitive individuals, contribute to kidney stones or other symptoms. Cooking reduces oxalate content, and some people following the Autoimmune Protocol choose to moderate high-oxalate foods.

Oxidative stress

Oxidative stress is an imbalance in which reactive molecules called free radicals outpace the body's antioxidant defenses, leading to damage at the cellular level. It is considered a contributing factor in autoimmune disease and chronic inflammation, part of why colorful, antioxidant-rich produce is emphasized in this way of eating.

Reference: Mitochondria reactive oxygen species signaling-dependent immune responses in macrophages and T cells. (Immunity, 2025) via PubMed

Pan drippings

Pan drippings are the flavorful juices and rendered fat left in a pan after roasting or searing meat. They form the base for a quick sauce or gravy, often deglazed with broth or an Autoimmune Protocol-friendly liquid to lift the browned bits from the bottom of the pan.

Pancreatic elastase

Pancreatic elastase is a digestive enzyme that can be measured in a stool test to check how well the pancreas is producing digestive enzymes. A low result suggests the pancreas may not be keeping up with digestion, which can leave food incompletely broken down and contribute to gut symptoms.

Reference: AGA Clinical Practice Update on the Epidemiology, Evaluation, and Management of Exocrine Pancreatic Insufficiency: Expert Review. (Gastroenterology, 2023) via PubMed

Pandan

Pandan is a fragrant tropical leaf, also called screwpine, used throughout Southeast Asian cooking to add a sweet, grassy aroma to rice, desserts, and drinks. The leaves themselves are usually steeped or blended for their scent rather than eaten directly.

See also: On the food list

Paprika

Paprika is a red spice ground from dried peppers and used to season stews, roasted meats, and vegetables. It belongs to the nightshade family, so it is set aside during the elimination phase of the Autoimmune Protocol and tested during reintroduction.

Parasympathetic nervous system

The parasympathetic nervous system is the branch of the nervous system often described as rest and digest, which calms the body, slows the heart rate, and supports digestion and tissue repair. Activating it through practices like slow breathing is considered supportive for people managing autoimmune disease and chronic stress.

Reference: Anti-inflammatory properties of the vagus nerve: potential therapeutic implications of vagus nerve stimulation. (The Journal of physiology, 2016) via PubMed

Parboil

To parboil means to partly cook a food, often a vegetable, by boiling it briefly before finishing it another way, such as roasting or frying. It shortens the final cooking time and can soften tougher vegetables before they go into a dish.

Parietal cell antibodies

Parietal cell antibodies are immune proteins that target the acid-producing cells of the stomach lining. Their presence is a marker of autoimmune gastritis, a condition that can reduce stomach acid and intrinsic factor production and lead to poor absorption of vitamin B12 and iron over time.

Reference: Autoimmune gastritis. (Nature reviews. Disease primers, 2020) via PubMed

Parsnip

A parsnip is a pale, cream-colored root vegetable that looks like a large carrot, with a sweet, earthy flavor that deepens when roasted. It works in soups, mashes, and roasted vegetable mixes throughout the Autoimmune Protocol.

See also: On the food list

Passionfruit

Passionfruit is a small tropical fruit with a wrinkled outer shell and fragrant, tart, seed-filled pulp inside. The pulp is scooped out and eaten directly, added to smoothies, or strained for its juice.

See also: On the food list

Pate

Pate is a smooth, spreadable mixture made from cooked, blended meat, often liver, sometimes combined with fat and herbs. It is an approachable way to work organ meats into the diet for anyone who finds liver on its own hard to enjoy.

See also: On the food list

Pawpaw

Pawpaw is a North American fruit with soft, custard-like yellow flesh and a flavor often described as a cross between banana and mango. It grows wild in parts of the eastern United States and is usually eaten fresh, since it does not ship or store well.

See also: On the food list

PCOS (polycystic ovary syndrome)

PCOS, or polycystic ovary syndrome, is a hormonal condition linked to insulin resistance, higher levels of androgens, and cycles that often do not ovulate regularly. It affects metabolism, skin, and fertility, and can overlap with autoimmune thyroid conditions, which is why it often comes up in functional medicine intake.

Reference: The interplay of oxidative stress and immune dysfunction in Hashimoto's thyroiditis and polycystic ovary syndrome: a comprehensive review. (Frontiers in immunology, 2023) via PubMed

Pectin

Pectin is a natural fiber found in fruit, especially apples and citrus peel, that thickens and sets jams and jellies as they cook. It also acts as a prebiotic fiber that feeds beneficial gut bacteria, and is used in moderate amounts on the Autoimmune Protocol.

See also: On the food list

Pepino

A pepino is a mild, sweet fruit with a melon-like flavor and smooth, striped skin. It belongs to the nightshade family, so it is avoided during the elimination phase of the Autoimmune Protocol and tested later during reintroduction.

See also: On the food list

Perilla

Perilla, also called shiso, is an aromatic leaf with a flavor that blends mint, basil, and anise. It is used fresh in Korean and Japanese cooking, wrapped around rice or grilled meat, or pickled as a side dish.

See also: On the food list

Perimenopause

Perimenopause is the transition period before menopause, often lasting several years, during which estrogen and progesterone fluctuate and decline unevenly rather than dropping in a straight line. The hormonal swings of this stage can intersect with autoimmune symptoms, which is why tracking cycle changes matters during this window.

Reference: Management of perimenopausal and menopausal symptoms. (BMJ, 2023) via PubMed

Peripheral conversion

Peripheral conversion is the process of turning the storage thyroid hormone T4 into the active hormone T3, which happens mainly in body tissues such as the liver, gut, and muscles rather than in the thyroid gland itself. Gut health and inflammation can interfere with this conversion, which matters for autoimmune thyroid disease.

Reference: The hypothalamus-pituitary-thyroid axis in critical illness. (The Netherlands journal of medicine, 2009) via PubMed

Persian melon

A Persian melon is a large, round melon with a netted rind similar to cantaloupe and sweet, orange flesh. It is eaten fresh, chilled, and cut into wedges or cubes.

See also: On the food list

Persimmon

Persimmon is a sweet orange fruit that comes in two main kinds. Astringent varieties like Hachiya must be eaten only when very soft and jelly-ripe, while non-astringent varieties like Fuyu can be eaten firm, sliced like an apple.

See also: On the food list

Pho

Pho is a Vietnamese soup built on a long-simmered, aromatic broth, usually beef or chicken, served with thin slices of meat and fresh herbs. An Autoimmune Protocol version leans on the broth and herbs while leaving out noodles and any nightshade-based garnishes.

See also: On the food list

Phthalates

Phthalates are a group of chemicals used to soften plastics and to help fragrances last, found in some food packaging, personal care products, and household items. They are studied as endocrine disruptors, meaning they can interfere with hormone signaling, a concern for anyone managing autoimmune or hormonal conditions.

Reference: Endocrine-disrupting chemicals and autoimmune diseases. (Environmental research, 2023) via PubMed

Phytates (phytic acid)

Phytates, or phytic acid, are compounds found in seeds, grains, and legumes that bind minerals such as iron, zinc, and calcium and can reduce how much the body absorbs from a meal. Soaking, sprouting, and fermenting traditionally reduce phytate content, though grains and legumes are set aside on the Autoimmune Protocol.

Pimento

A pimento is a sweet, mild red pepper, most familiar as the small piece stuffed into green olives. It is a nightshade, so it is avoided during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Plantain

Plantain is a large, starchy relative of the banana that is cooked rather than eaten raw. Green plantains behave like a starchy vegetable, similar to a potato, while ripe, yellow-black plantains turn soft and sweet, and both are staple Autoimmune Protocol starches.

Plantain flour

Plantain flour is a grain-free flour made by drying and grinding green plantains, used in baking, as a thickener for sauces, and to bread meat or fish. It is a common pantry staple on the Autoimmune Protocol for recreating familiar textures without grain.

See also: On the food list

PMDD (premenstrual dysphoric disorder)

PMDD, or premenstrual dysphoric disorder, is a severe form of premenstrual symptoms marked by significant mood changes, including irritability, anxiety, or low mood, in the days before a period. It is thought to reflect an unusual sensitivity to normal hormone shifts in the luteal phase rather than abnormal hormone levels themselves.

Reference: Neurosteroids and premenstrual dysphoric disorder. (The British journal of psychiatry, 2025) via PubMed

PMS (premenstrual syndrome)

PMS, or premenstrual syndrome, is a cluster of physical and emotional symptoms, such as bloating, breast tenderness, irritability, or fatigue, that shows up in the days before a period. It is often linked to the shifting balance of estrogen and progesterone across the cycle, and inflammation can make symptoms more intense.

Reference: Management of Premenstrual Disorders: ACOG Clinical Practice Guideline No. 7. (Obstetrics and gynecology, 2023) via PubMed

Poach

To poach means to cook food gently in liquid kept just below a simmer, hot enough to cook through but too gentle to toughen delicate proteins. It is a favorite method for fish, chicken, and eggs on the Autoimmune Protocol.

Pointed gourd

Pointed gourd, also called parwal or parval, is a small, green, oval gourd common in Indian cooking. It has a mild flavor and is usually stuffed, stir-fried, or simmered into a curry.

See also: On the food list

Poke bowl

A poke bowl is a Hawaiian dish built around cubes of seasoned raw fish, traditionally tuna, served over a base with vegetables and toppings. An Autoimmune Protocol version swaps rice for cauliflower rice or greens and skips soy sauce and sesame for compliant seasonings.

See also: On the food list

Polyphenol

Polyphenols are a large group of plant compounds found in colorful fruits, vegetables, herbs, and spices. They act as antioxidants and also feed beneficial gut bacteria, and diets rich in polyphenols are associated with lower inflammation, part of why colorful produce is emphasized on the Autoimmune Protocol.

Reference: Polyphenols: food sources and bioavailability. (The American journal of clinical nutrition, 2004) via PubMed

Pomelo

A pomelo is the largest citrus fruit, with a thick, easy-to-peel rind and mild, sweet flesh. It is a relative of the grapefruit but less bitter, and can be eaten in segments or added to salads.

See also: On the food list

Porcini

Porcini are meaty, nutty wild mushrooms often sold dried, which concentrates their flavor for use in broths, sauces, and braises. A small amount of soaked dried porcini can add deep, savory flavor to an Autoimmune Protocol dish without needing added seasoning blends.

See also: On the food list

Portobello

A portobello is a large, mature brown mushroom with a dense, meaty texture that holds up well to grilling or roasting. Its size and texture make it a satisfying stand-in for a more substantial main course.

See also: On the food list

Postbiotic

Postbiotics are the beneficial compounds, including short-chain fatty acids like butyrate, that gut bacteria produce when they ferment fiber from food. These compounds help nourish the cells lining the colon and support a healthy gut barrier, a central concern in autoimmune gut healing.

Reference: Postbiotics and Their Health Modulatory Biomolecules. (Biomolecules, 2022) via PubMed

Poultry fat

Poultry fat is the rendered fat from chicken, duck, or goose, saved from roasting or purchased separately as schmaltz or duck fat. It is a stable cooking fat well suited to sauteing and roasting on the Autoimmune Protocol.

See also: On the food list

Prebiotic

Prebiotics are a type of fiber that the body cannot digest but that beneficial gut bacteria can ferment and use as fuel. Foods such as onion, garlic, plantain, and cooked-and-cooled starches supply prebiotic fiber, and feeding the right bacteria is part of restoring gut balance in autoimmune healing.

Reference: Complex regulatory effects of gut microbial short-chain fatty acids on immune tolerance and autoimmunity. (Cellular & molecular immunology, 2023) via PubMed

Pregnenolone

Pregnenolone is a precursor hormone made from cholesterol that the body uses as the starting material to build cortisol, DHEA, and the sex hormones. Because it sits upstream of so many other hormones, its availability can influence the whole hormonal cascade, including for people managing autoimmune and adrenal stress.

Reference: The molecular biology, biochemistry, and physiology of human steroidogenesis and its disorders. (Endocrine reviews, 2010) via PubMed

Pregnenolone steal

Pregnenolone steal is a proposed model in which ongoing physical or emotional stress shifts the body's hormone production toward cortisol at the expense of the sex hormones. It remains a clinical concept used by some functional medicine practitioners rather than a fully settled physiological mechanism, worth naming plainly as such.

Probiotic

Probiotics are live beneficial bacteria, found in fermented foods such as sauerkraut and coconut yogurt or taken as a supplement, that can help support a healthy balance of microbes in the gut. Restoring that balance is one piece of the gut healing work often paired with the Autoimmune Protocol.

Reference: Emerging role of gut microbiota in autoimmune diseases. (Frontiers in immunology, 2024) via PubMed

Progesterone

Progesterone is a sex hormone produced mainly after ovulation, during the second half of the menstrual cycle. It has a calming effect on the nervous system and helps regulate immune activity, and low progesterone relative to estrogen is a pattern that often comes up in autoimmune and hormonal case histories.

Reference: Hormones and B-cell development in health and autoimmunity. (Frontiers in immunology, 2024) via PubMed

Proline

Proline is an amino acid, plentiful in foods like bone broth and slow-cooked cuts of meat with connective tissue, that serves as a key building block of collagen. Collagen forms much of the structural tissue in joints, skin, and the gut lining, which is why broth is a staple on the Autoimmune Protocol.

Proof

To proof means to let a yeasted dough or batter rest in a warm spot so it can rise before baking. The resting time allows the yeast to produce gas that gives the finished food its lift and texture.

Proton pump inhibitor

A proton pump inhibitor is a common class of medication, including omeprazole, that lowers stomach acid production to treat reflux or ulcers. Long-term use is linked to reduced absorption of nutrients such as B12, magnesium, and iron, worth discussing with a prescribing doctor rather than adjusting alone.

Reference: The Risks and Benefits of Long-term Use of Proton Pump Inhibitors: Expert Review and Best Practice Advice From the American Gastroenterological Association. (Gastroenterology, 2017) via PubMed

Pseudo-grain

A pseudo-grain is a seed that is cooked and eaten like a grain even though it does not come from a grass plant, such as quinoa, buckwheat, or amaranth. All grains and pseudo-grains are set aside during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Psoriasis

Psoriasis is an autoimmune-related skin condition in which the immune system speeds up skin cell turnover, causing cells to build up faster than they can shed and forming thick, scaly, often itchy patches. It is a chronic inflammatory condition that can flare and settle in response to stress, diet, and other triggers.

Reference: Risk Factors for the Development of Psoriasis. (International journal of molecular sciences, 2019) via PubMed

Psoriatic arthritis

Psoriatic arthritis is a form of inflammatory arthritis that can develop in some people who have psoriasis, in which the immune system also attacks the joints, causing pain, stiffness, and swelling. It is classified as an autoimmune condition and can cause joint damage over time if inflammation is not addressed.

Reference: Psoriatic arthritis from a mechanistic perspective. (Nature reviews. Rheumatology, 2022) via PubMed

Purple yam

Purple yam, also called ube, is a bright purple, starchy tuber popular in Filipino cooking, used in both savory dishes and sweet desserts. It has a mildly sweet, nutty flavor and can be boiled, roasted, or mashed like other starchy root vegetables on the Autoimmune Protocol.

See also: On the food list

Purslane

Purslane is a low-growing succulent green with small, juicy leaves and a slightly tart, lemony flavor. It is one of the few plant sources of omega-3 fat and can be eaten raw in salads or lightly cooked.

See also: On the food list

Quince

Quince is a hard, fragrant fruit related to the apple and pear that is too astringent to eat raw. Cooking softens it and brings out a rosy color and floral sweetness, making it a good choice for compotes, pastes, and slow-baked desserts.

See also: On the food list

Radicchio

Radicchio is a red-and-white leafy chicory with a bitter, peppery bite. It can be eaten raw in salads for texture and contrast or grilled briefly, which mellows the bitterness and brings out a smoky sweetness.

See also: On the food list

Rambutan

Rambutan is a small tropical fruit covered in a hairy red shell, with sweet, juicy, translucent flesh similar to lychee inside. The shell is peeled away and the seed removed before eating the fruit fresh.

See also: On the food list

Ramp

A ramp is a wild spring onion, also called a wild leek, with a strong garlic-onion flavor and broad green leaves. Ramps have a short foraging season and are often sauteed, pickled, or used raw in place of milder alliums.

Reactive hypoglycemia

Reactive hypoglycemia is a drop in blood sugar that occurs a few hours after eating, often following a meal high in refined carbohydrates. The resulting dip can trigger a stress and cortisol response, with symptoms like shakiness, irritability, or fatigue, and steadying blood sugar is a recurring theme in autoimmune care.

Reference: Postprandial Reactive Hypoglycemia. (Sisli Etfal Hastanesi tip bulteni, 2019) via PubMed

Reduce

To reduce means to simmer a liquid, such as broth or a sauce, uncovered so that some of the water evaporates, leaving a smaller volume that is thicker and more concentrated in flavor.

Reduction

A reduction is the thickened, concentrated liquid that results from simmering a sauce, broth, or juice down to a smaller volume. It is used to build flavor into a finished dish without needing added thickeners.

Reference range

A reference range is the span of lab results a lab marks as normal, based on values drawn from a general population rather than from people at optimal health. It does not represent the ideal or most functional level for a marker, only the statistical middle. A result inside the reference range can still fall short of what supports full healing.

Regulatory T cells (Tregs)

Regulatory T cells, or Tregs, are immune cells that calm the immune response and help the body tell its own tissue apart from a genuine threat. This tolerance function keeps immune activity from turning on healthy organs and joints. In autoimmune disease, Treg numbers or activity are often reduced, part of how self-tolerance breaks down.

Reference: Regulatory T Cells and Human Disease. (Annual review of immunology, 2020) via PubMed

Reintroduction

Reintroduction is the second phase of the Autoimmune Protocol, when previously removed foods are added back one at a time, in a set order, with days between each addition. The slow pace allows a reaction, if one appears, to be traced to a single food rather than a mix. It turns a strict elimination diet into a personalized, longer term way of eating.

Remission

Remission is a state in which autoimmune symptoms quiet down substantially and energy, digestion, and daily function return, even though the underlying disease process may still be present at a low level. It differs from a cure, which implies the disease is gone entirely. For most people managing autoimmune disease, remission is the realistic, meaningful goal.

Reference: Defining immune reset: achieving sustained remission in autoimmune diseases. (Nature reviews. Immunology, 2025) via PubMed

Render

Rendering is the process of melting solid animal fat slowly over low heat until the pure fat separates from any connective tissue or bits of meat. The liquid fat is then strained and saved for cooking. Lard, tallow, and schmaltz are all products of rendering.

Resistant starch

Resistant starch is a type of starch that passes through the small intestine largely undigested and reaches the colon, where gut bacteria ferment it into short-chain fatty acids. Those fatty acids feed the cells lining the gut and support a healthy microbial balance. Cooked-and-cooled tubers and green plantains are common sources.

Reference: Impact of Dietary Fiber on Inflammation in Humans. (International journal of molecular sciences, 2025) via PubMed

Reverse T3 (rT3)

Reverse T3 is an inactive mirror image of active thyroid hormone, made when the body shunts T4 down a different conversion pathway instead of turning it into T3. It can occupy the same receptor sites as active hormone without switching them on, effectively blocking the signal. It tends to rise under prolonged stress, illness, or inflammation.

Reference: Non-thyroidal illness in the ICU: a syndrome with different faces. (Thyroid : official journal of the American Thyroid Association, 2014) via PubMed

Rheumatoid arthritis

Rheumatoid arthritis is an autoimmune condition in which the immune system attacks the lining of the joints, causing pain, swelling, and stiffness often worse in the morning. Left unmanaged, ongoing inflammation can erode cartilage and bone and lead to lasting joint damage. It is one of the more common autoimmune diseases addressed with diet and lifestyle work.

Reference: Effect of Anti-Inflammatory Diets on Pain in Rheumatoid Arthritis: A Systematic Review and Meta-Analysis. (Nutrients, 2021) via PubMed

Rhizome

A rhizome is a thick underground stem that grows horizontally and sends up shoots, distinct from a true root. Ginger, turmeric, galangal, and fingerroot are all rhizomes used fresh, dried, or ground as seasoning. Their strong flavor and color come from compounds concentrated in that stem.

Ridge gourd

Ridge gourd is a long, ridged green gourd also known as luffa, turai, or Chinese okra. It is harvested and cooked while still young and tender, since older gourds turn fibrous. It works well stir-fried, simmered in curry, or added to soups.

See also: On the food list

Romanesco

Romanesco is a pale green vegetable with a striking spiral, cone-shaped head, closely related to both cauliflower and broccoli. Its flavor is milder and nuttier than either relative. It roasts, steams, or sautes well and tends to hold its shape better than cauliflower once cooked.

See also: On the food list

Rooibos tea

Rooibos is a naturally caffeine-free herbal tea made from a South African shrub, with a reddish color and a mild, slightly sweet, earthy flavor. Because it contains no caffeine, it is a common substitute for black or green tea during elimination. It can be served hot or iced.

See also: On the food list

Rose apple

Rose apple, also called wax apple or jambu, is a crisp, watery tropical fruit with a light floral aroma and a mildly sweet taste. Its thin skin ranges from pale green to deep red, and it is eaten fresh, skin and all. The texture is closer to a crunchy pear than a typical apple.

See also: On the food list

Rosehip

Rosehip is the small, round fruit left behind on a rose bush after the flower drops its petals. It is dried and steeped for tea, or cooked down into syrup or jam, and is known as a natural source of vitamin C. Its flavor is tart and slightly fruity.

See also: On the food list

Roux

A roux is a cooked paste of fat and flour used as a base to thicken sauces, gravies, and soups. On the Autoimmune Protocol it is made with a grain-free flour such as arrowroot or cassava instead of wheat flour. The fat and flour cook together briefly before liquid is whisked in.

Rutabaga

Rutabaga is a round root vegetable in the cabbage family, a cross between cabbage and turnip, with sweeter, denser flesh than either parent. It is roasted, mashed, or added to stews as a potato substitute. Its pale yellow flesh and thick skin distinguish it from a true turnip.

See also: On the food list

Salak

Salak, also called snake fruit for its scaly reddish-brown skin, is a small tropical fruit with firm, segmented, sweet-tart flesh. The skin is peeled away before eating, revealing flesh shaped somewhat like garlic cloves. It is native to Indonesia and popular throughout Southeast Asia.

See also: On the food list

Salivary cortisol test

A salivary cortisol test measures cortisol from saliva collected at several points across the day, typically on waking, midday, afternoon, and bedtime, to map the daily cortisol rhythm rather than a single snapshot. Because chronic stress and adrenal dysregulation can worsen autoimmune symptoms, this pattern often gives more useful information than one blood draw.

Reference: Measuring cortisol in serum, urine and saliva - are our assays good enough? (Annals of clinical biochemistry, 2017) via PubMed

Salmonberry

Salmonberry is a soft, juicy wild berry related to the raspberry, ranging in color from golden orange to deep red. It grows on thorny shrubs native to the Pacific Northwest and is eaten fresh or made into jam. Its flavor is mild and less tart than a raspberry.

See also: On the food list

Salo

Salo is cured, unrendered pork fat from Eastern European tradition, typically salted or smoked and sliced thin. It is eaten on its own, often with garlic and bread, or used as a cooking fat. It is prized for its clean, rich flavor rather than any meat content.

See also: On the food list

Salsify

Salsify is a long, slender root vegetable with pale flesh and a delicate flavor some compare to oysters, which is why it is also called oyster plant. It is peeled and cooked much like a parsnip, by roasting, mashing, or simmering in soup. Cut flesh discolors quickly and benefits from a quick soak in acidulated water.

See also: On the food list

Samphire

Samphire, also known as sea bean or glasswort, is a crisp, naturally salty plant that grows along coastal marshes and mudflats. It is eaten raw in salads or briefly blanched or sauteed, since its high natural salt content means little added seasoning is needed. Its texture is crunchy and slightly juicy.

See also: On the food list

Santol

Santol, sometimes called cotton fruit, is a round tropical fruit with a thick rind and sweet-sour flesh surrounding large seeds. It is eaten fresh, often dipped in salt, or used in Southeast Asian sweet and sour dishes. Flesh near the skin is more sour, while pulp closer to the seed is sweeter.

See also: On the food list

Sapodilla

Sapodilla, also called chiku or sapota, is a small brown tropical fruit with grainy, custard-like flesh and a flavor often compared to brown sugar and pear. It is only eaten fully ripe, since unripe fruit is astringent from natural tannins. The skin and large black seeds are discarded before eating.

See also: On the food list

Saponins

Saponins are plant-defense compounds found in legumes, pseudo-grains like quinoa, and some nightshades, named for the soapy foam they produce in water. They can bind to the gut lining and increase its permeability, one reason legumes and pseudo-grains are removed during the elimination phase of the Autoimmune Protocol. Cooking and soaking reduce saponin content but do not eliminate it.

Reference: Immunomodulatory potential of dietary soybean-derived saponins. (Journal of animal science, 2024) via PubMed

Sauerkraut

Sauerkraut is finely shredded cabbage that has been salted and left to ferment until it turns tangy and slightly effervescent. Fermentation produces beneficial bacteria, making it a traditional, food-based source of probiotics. It is typically introduced only after the gut has had time to stabilize.

Saute

To saute is to cook food quickly in a small amount of fat over fairly high heat, stirring or tossing it frequently in the pan. The technique browns food lightly while keeping the inside tender, and it works well for vegetables, aromatics, and thin cuts of meat. It requires more attention at the stove than roasting.

Savory herb

Savory is a peppery, slightly bitter herb with a flavor that sits somewhere between thyme and mint. It is traditionally paired with bean dishes for its reputed digestive benefit and is also used in meats, stuffing, and soups. Summer and winter varieties both exist, with winter savory having the stronger flavor.

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Scallion

Scallion, also called green onion, is a young onion harvested before its bulb fully forms, leaving a small white base and long green stalks. Both the white and green parts are edible, raw or cooked, and offer a milder bite than a mature onion. It is used as a garnish as well as a cooking ingredient.

See also: On the food list

Schmaltz

Schmaltz is rendered chicken or goose fat, traditionally seasoned with onion and used both as a cooking fat and as a flavor-rich addition to other dishes. It has a savory, rich taste that plain vegetable oils lack. On the Autoimmune Protocol it is a well-tolerated animal fat for sauteing and roasting.

See also: On the food list

Scorzonera

Scorzonera, also called black salsify, is a long root vegetable with dark, almost black skin and pale flesh with a mild, slightly sweet flavor similar to salsify. It is peeled and cooked by roasting, steaming, or simmering. Like salsify, its cut flesh discolors quickly and benefits from a quick soak in acidulated water.

See also: On the food list

Sea buckthorn

Sea buckthorn is a small, tart orange berry that grows on a hardy shrub, most often used as juice, puree, or oil rather than eaten whole off the branch. It is known as a concentrated source of vitamins and antioxidant compounds. Its flavor is sharp and sour, so it is usually diluted or lightly sweetened.

See also: On the food list

Sea kale

Sea kale is a coastal leafy vegetable with thick, pale stems and mild-flavored leaves, related to cabbage despite its different look. It is cooked much like other leafy greens, by steaming, sauteing, or braising. Young, blanched shoots are considered the most tender part of the plant.

See also: On the food list

Sea vegetables

Sea vegetables are edible plants harvested from the ocean, including nori, kombu, wakame, and dulse. They add a natural savory flavor to broths and dishes and are a notable food source of iodine and other minerals. They are used in modest amounts, since iodine intake needs to stay balanced for thyroid health.

See also: On the food list · Preparing to start

Sear

Searing is cooking the surface of meat, poultry, or fish over high heat for a short time so it browns deeply and develops flavor before the interior is fully cooked. It is often the first step in a recipe, followed by finishing in the oven, a slow cooker, or a braise. The goal is color and flavor, not doneness.

Secretory IgA

Secretory IgA is an antibody produced by cells lining the gut that acts as a first line of immune defense there, binding to pathogens and food proteins before they can penetrate the intestinal wall. It is sometimes measured on stool or gut testing as a marker of gut immune activity. Levels that are too low or too high can both point to gut immune imbalance worth investigating.

Reference: Secretory IgA's complex roles in immunity and mucosal homeostasis in the gut. (Mucosal immunology, 2011) via PubMed

Selenium

Selenium is a trace mineral the thyroid depends on both to produce thyroid hormone and to convert it into its active form, and it also helps limit thyroid antibody levels in autoimmune thyroid disease. Brazil nuts and seafood are natural sources, though nuts are avoided during the elimination phase of the Autoimmune Protocol. Selenium status is often relevant for anyone managing Hashimoto's.

Reference: Selenium Supplementation in Patients with Hashimoto Thyroiditis: A Systematic Review and Meta-Analysis of Randomized Clinical Trials. (Thyroid : official journal of the American Thyroid Association, 2024) via PubMed

Serotonin

Serotonin is a neurotransmitter best known for its role in mood, though most of the body's serotonin is actually produced in the gut, where it helps regulate digestion and motility. Gut health and serotonin production are closely linked, part of why gut healing can affect mood. This gut-brain connection is a growing area of research in autoimmune disease.

Reference: Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. (Behavioural brain research, 2014) via PubMed

Serum iron

Serum iron measures the amount of iron currently circulating in the bloodstream at the moment blood is drawn. It differs from ferritin, which reflects the body's stored iron reserves, and the two are usually interpreted together for a fuller picture. Serum iron can fluctuate with recent meals, time of day, and inflammation.

Sex hormone binding globulin (SHBG)

Sex hormone binding globulin, or SHBG, is a protein made mainly by the liver that binds estrogen and testosterone in the bloodstream, carrying them while keeping them inactive. When SHBG is high, less free hormone reaches tissue and does its work, even if total hormone levels look normal on a lab report. SHBG is influenced by thyroid status, insulin, and inflammation, all relevant in autoimmune disease.

Reference: Recent Advances on Sex Hormone-Binding Globulin Regulation by Nutritional Factors: Clinical Implications. (Molecular nutrition & food research, 2024) via PubMed

Shallot

Shallot is a small, elongated member of the onion family with a mild, slightly sweet, more delicate flavor than a regular onion. Its cloves separate somewhat like garlic, though it is used in cooking much like an onion. It is common in dressings, sauces, and quick sautes where a subtler onion flavor is wanted.

See also: On the food list

Shawarma

Shawarma is a Middle Eastern dish of meat, often lamb, chicken, or beef, seasoned with a warm spice blend and traditionally cooked on a vertical rotisserie before being sliced thin. It can also be made at home in a skillet or oven using the same style of seasoning. An Autoimmune Protocol version swaps out nightshade and seed spices for approved alternatives.

Sheet-pan

Sheet-pan cooking is a method where a whole meal, usually a protein and a mix of vegetables, is arranged on one flat baking tray and roasted together in the oven. It is a low-effort way to get a balanced meal on the table with minimal cleanup. Cutting vegetables to a similar size helps everything finish together.

Shiitake

Shiitake is a brown, meaty East Asian mushroom with a deep, savory flavor, sold fresh or dried. Dried shiitakes are often reconstituted in water, and the soaking liquid is saved for its concentrated flavor in broths and sauces. They are used widely in soups, stir-fries, and braises.

See also: On the food list

Short-chain fatty acids

Short-chain fatty acids are compounds gut bacteria produce when they ferment dietary fiber, including butyrate, acetate, and propionate. They are a primary fuel source for the cells lining the colon and play a role in regulating inflammation and immune activity throughout the body. Supporting their production through fiber-rich foods is one way diet influences gut and immune health.

Reference: Short-chain fatty acids: linking diet, the microbiome and immunity. (Nature reviews. Immunology, 2024) via PubMed

SIBO (small intestinal bacterial overgrowth)

SIBO occurs when bacteria that normally live mostly in the large intestine grow in excess in the small intestine, where they can ferment food too early and produce gas. It is more common in people with low thyroid function and can drive bloating, discomfort, and reactions to foods that would otherwise be well tolerated. Identifying and addressing SIBO is often a key step in resolving stubborn gut symptoms.

Reference: AGA Clinical Practice Update on Small Intestinal Bacterial Overgrowth: Expert Review. (Gastroenterology, 2020) via PubMed

Sjogren's syndrome

Sjogren's syndrome is an autoimmune condition in which the immune system attacks the glands that produce moisture, most often causing chronic dry eyes and dry mouth. It can also affect joints, skin, and other organs, and often occurs alongside other autoimmune conditions. Because dryness symptoms can be subtle at first, it is sometimes diagnosed only after years of symptoms.

Reference: Manifestations and management of Sjögren's disease. (Arthritis research & therapy, 2024) via PubMed

Slow cooker

A slow cooker is a countertop appliance that cooks food gently at a low, steady temperature over many hours, usually with a lid to trap moisture. It suits stews, broths, and braises well, since the long, gentle cooking time tenderizes tougher cuts of meat and develops deep flavor with little hands-on effort.

Snake gourd

Snake gourd is a long, thin, pale green gourd, also called chichinda or padwal, common in South and Southeast Asian cooking. It is harvested young and tender, then cooked in curries, stir-fries, or stuffed dishes. Its mild flavor takes on whatever seasonings it is cooked with.

See also: On the food list

Sofrito

Sofrito is a cooked base of finely chopped aromatic vegetables and herbs, slowly cooked in fat until soft and fragrant, used to build flavor at the start of many Latin American and Mediterranean dishes. The exact vegetables vary by region and cook. An Autoimmune Protocol sofrito leaves out nightshades like tomato and bell pepper.

Solanaceae

Solanaceae is the botanical family name for nightshades, a group of plants that includes tomatoes, potatoes, eggplant, and peppers. All nightshade foods share this classification and are removed together during the elimination phase of the Autoimmune Protocol. Knowing the family helps with reading ingredient lists, since nightshade-derived items like paprika and chili powder are easy to miss.

Sorghum

Sorghum is a mild, gluten-free grain that can be eaten whole, popped like popcorn, or ground into flour for baking. As a grain, it is excluded during the elimination phase of the Autoimmune Protocol along with other grains, even though it contains no gluten. Some people reintroduce it later and tolerate it well.

See also: On the food list

Sorrel

Sorrel is a leafy green herb with a sharp, lemony, almost tart flavor that comes from naturally occurring oxalic acid. It is used in soups, sauces, and salads, often in small amounts because its flavor is strong. French sorrel soup is a classic way it is used.

See also: On the food list

Soursop

Soursop, also called guanabana, is a large, spiny-skinned tropical fruit with soft, tangy-sweet white flesh and large black seeds that are discarded. It is eaten fresh with a spoon, blended into drinks, or made into ice cream and sorbet. Its flavor is often described as a mix of strawberry, pineapple, and citrus.

See also: On the food list

Soy lecithin

Soy lecithin is a fatty substance extracted from soybeans and used as an emulsifier to help blend fat and water together smoothly in many packaged and processed foods. Because it is derived from soy, it is avoided on the Autoimmune Protocol, and it appears on ingredient labels for items like chocolate, dressings, and baked goods.

Spaghetti squash

Spaghetti squash is a winter squash whose cooked flesh pulls apart into long, thin strands resembling noodles. It is roasted or steamed whole or in halves, then scraped out with a fork, and works as a grain-free substitute for pasta. Its mild flavor takes on whatever sauce or seasoning it is paired with.

See also: On the food list

Spatchcock

To spatchcock a bird is to remove its backbone with kitchen shears and press it flat, so the whole bird cooks faster and more evenly than it would whole. It is a common technique for roasting chicken or turkey, since the flattened shape exposes more skin to heat and shortens cooking time.

Spelt

Spelt is an ancient variety of wheat, related closely enough to modern wheat that it still contains gluten. Despite sometimes being marketed as easier to digest, it is not gluten-free and is excluded on any gluten-free or Autoimmune Protocol diet. It is used in some traditional breads and pastas.

See also: On the food list

Spiralize

To spiralize is to cut a vegetable, such as zucchini or sweet potato, into long, thin, noodle-like strands using a spiralizer tool or attachment. The resulting strands can be eaten raw in salads or lightly cooked as a grain-free swap for pasta.

Spiralizer

A spiralizer is a kitchen tool, either handheld or countertop, that cuts firm vegetables into long, curling, noodle-like strands. It is a common way to turn zucchini, carrots, or sweet potato into a grain-free pasta substitute with minimal effort.

Squash blossom

Squash blossom is the edible flower produced by squash and zucchini plants before the fruit forms. It has a delicate, slightly sweet flavor and is often stuffed, fried in a light coating, or added raw to salads. Blossoms are fragile and best used the same day they are picked.

See also: On the food list

Star anise

Star anise is a star-shaped seed pod with a strong, sweet, licorice-like flavor, used whole or ground in braises, broths, and spice blends. A single pod goes a long way, since its flavor is potent. It is common in Chinese five-spice and many slow-cooked meat dishes.

See also: On the food list

Star fruit

Star fruit, or carambola, is a waxy yellow tropical fruit that forms a distinct star shape when sliced crosswise. Its flavor is crisp and mildly tart, somewhere between grape and citrus, and the skin is eaten along with the flesh. It is often used as a garnish as well as a fruit on its own.

See also: On the food list

Stomach acid (hydrochloric acid)

Stomach acid, or hydrochloric acid, is the strong acid the stomach produces to begin breaking down protein and to create the acidic environment needed to absorb minerals like iron and vitamin B12. Low stomach acid, sometimes called hypochlorhydria, is common and often overlooked, and it can lead to poor digestion, bloating, and nutrient deficiencies that matter during autoimmune recovery.

Reference: Rationale in diagnosis and screening of atrophic gastritis with stomach-specific plasma biomarkers. (Scandinavian journal of gastroenterology, 2012) via PubMed

Streptococcus

Streptococcus is a family of bacteria whose surface proteins can closely resemble proteins found in heart, joint, or brain tissue. When the immune system mounts a response to a streptococcal infection, it can mistakenly target those look-alike tissues too, a process called molecular mimicry. This mechanism is studied as one possible trigger for certain autoimmune conditions.

Reference: The intricate pathogenicity of Group A: A comprehensive update. (Virulence, 2024) via PubMed

Strutto

Strutto is the Italian name for rendered pork fat, similar to lard, traditionally used for frying, roasting, and enriching pastry. It has a clean, mild flavor and a high smoke point, which makes it useful for high-heat cooking.

See also: On the food list

Subclinical hypothyroidism

Subclinical hypothyroidism is an early pattern of thyroid dysfunction in which TSH is mildly elevated while free T4 still falls within the standard reference range. Symptoms of low thyroid function, such as fatigue, cold intolerance, or brain fog, can be present even though the labs look only borderline. It is worth tracking over time rather than dismissing because it technically falls within range.

Reference: Treating hypothyroidism is not always easy: When to treat subclinical hypothyroidism, TSH goals in the elderly, and alternatives to levothyroxine monotherapy. (Journal of internal medicine, 2021) via PubMed

Sugar apple

Sugar apple, also called sweetsop or custard apple, is a knobby, greenish tropical fruit with soft, sweet, creamy segments of flesh surrounding shiny black seeds. It is eaten fresh with a spoon once fully ripe and soft to the touch. Its flavor is often compared to a blend of banana and pineapple.

See also: On the food list

Sumac

Sumac is a tangy, deep red Middle Eastern spice made from the dried, ground berries of the sumac shrub. It adds a bright, lemony sourness to dishes without any citrus, and is commonly sprinkled over salads, meats, and dips. It is a staple in za'atar spice blends.

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Sympathetic nervous system

The sympathetic nervous system is the branch of the nervous system responsible for the body's fight-or-flight response, raising heart rate, redirecting blood flow, and preparing the body for action under stress. Chronic activation from ongoing physical or emotional stress can suppress digestion and drive the kind of low-grade inflammation that worsens autoimmune symptoms over time. Shifting toward the rest-and-digest state is a core piece of autoimmune recovery.

Reference: Neuroimmune Crosstalk in Rheumatoid Arthritis. (International journal of molecular sciences, 2022) via PubMed

Synthetic progestins

Synthetic progestins are lab-made compounds used in many forms of hormonal birth control and some hormone therapies, designed to act on progesterone receptors even though their molecular structure differs from the body's own progesterone. Because of that structural difference, they do not always produce the same effects, and some research has linked certain progestins to changes in mood and immune activity. This distinction matters when reviewing hormone history as part of autoimmune care.

Reference: Hormonal modulation of the immune system - A spotlight on the role of progestogens. (Autoimmunity reviews, 2015) via PubMed

T cell

A T cell is a type of white blood cell central to the immune system, with different subtypes that either coordinate the overall immune response or directly attack cells identified as a threat. In autoimmune disease, certain T cells mistakenly identify the body's own tissue as a threat and attack it. Understanding T cell behavior is central to understanding how autoimmune disease develops.

Reference: T cells in health and disease. (Signal transduction and targeted therapy, 2023) via PubMed

T3 (triiodothyronine)

T3, or triiodothyronine, is the active form of thyroid hormone, the form that actually enters cells and drives energy production, metabolism, body temperature, and mood. Most T3 is made by converting the storage hormone T4 in tissues throughout the body, not only in the thyroid gland itself. Because of this, T3 levels can be low even when thyroid gland function and TSH look normal on standard labs.

Reference: Thyroidal and peripheral production of thyroid hormones. Review of recent findings and their clinical implications. (Annals of internal medicine, 1977) via PubMed

T4 (thyroxine)

T4, or thyroxine, is the main hormone the thyroid gland releases into the bloodstream. It is a storage form that carries relatively little activity on its own until tissues throughout the body convert it into the active hormone T3.

T4-to-T3 conversion

T4-to-T3 conversion is the process of turning the thyroid's storage hormone into its active form, largely in the liver, gut, and other tissues rather than the thyroid itself. Chronic stress, inflammation, and gut or nutrient problems are associated with reduced conversion, which matters because low active hormone can persist even when standard thyroid labs look normal.

Reference: Non-thyroidal Illness Syndrome as an Adaptive Longevity Program: Reframing Low T3 in Acute and Chronic Disease. (Cureus, 2026) via PubMed

Tallow

Tallow is rendered fat from beef or lamb, solid at room temperature and stable at high heat, which makes it a reliable cooking fat for searing and frying. On the Autoimmune Protocol it is a well tolerated animal fat free of the plant compounds eliminated during the elimination phase.

Tamari

Tamari is a dark, savory sauce brewed from fermented soybeans, similar to soy sauce and sometimes made with little or no wheat. It is still a soy product, so it stays off the Autoimmune Protocol food list even when labeled gluten free.

See also: On the food list

Tamarillo

Tamarillo, also called tree tomato, is an egg-shaped tropical fruit with tart, juicy flesh eaten raw or cooked into sauces and chutneys. It belongs to the nightshade family, so it is excluded during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Tamarind

Tamarind is the sour, sticky pulp found inside the pods of a tropical tree, used to add tang to sauces, drinks, and curries. It is technically a legume, which places it outside core Autoimmune Protocol foods though many find it well tolerated on reintroduction.

See also: On the food list

Tangelo

Tangelo is a citrus fruit created by crossing a tangerine with a grapefruit or pomelo, prized for its juiciness and easy-to-peel skin. Citrus fruits are generally included on the Autoimmune Protocol food list in moderate amounts.

See also: On the food list

Tannins

Tannins are astringent plant compounds found in tea, red wine, and some fruits such as salak, responsible for the dry, puckery feeling they leave in the mouth. They are a normal part of many plant foods rather than a marker of quality or harm.

Tapenade

Tapenade is a thick, savory spread made by finely chopping olives, capers, and oil together, often with garlic or herbs. It works as a quick flavor boost for vegetables, meats, or crackers made from Autoimmune Protocol-friendly ingredients.

Tapioca

Tapioca is a starch extracted from the cassava root, sold as flour, pearls, or flakes. On the Autoimmune Protocol it is commonly used to thicken sauces and to give grain-free baked goods a chewy texture, though it offers little nutrition beyond starch.

Taro

Taro is a starchy tropical root vegetable with a mildly nutty flavor, prepared much like potato in soups, mashes, and fries. It contains compounds that irritate the mouth and gut when raw, so it must always be cooked thoroughly before eating.

Taro leaves

Taro leaves, also called luau leaf or dasheen leaf, are the broad green leaves of the taro plant, used as a cooked vegetable in island and Southeast Asian cooking. Like the root, they contain irritating compounds and must always be cooked thoroughly, never eaten raw.

See also: On the food list

Tatsoi

Tatsoi is a small, spoon-shaped Asian green with dark, glossy leaves and a mild, slightly mustardy flavor. It can be eaten raw in salads or lightly wilted into stir-fries and soups.

See also: On the food list

Teff

Teff is a tiny, gluten-free grain native to Ethiopia, traditionally ground into flour for injera flatbread or cooked into porridge. As a grain it falls outside core Autoimmune Protocol foods during the elimination phase.

See also: On the food list

Tempeh

Tempeh is a firm, nutty-tasting cake made by fermenting whole soybeans, used widely as a plant protein. It is a soy product, so it is excluded during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Temper

To temper means to warm an ingredient gradually rather than shocking it with sudden heat, such as slowly whisking hot broth into beaten eggs or gelatin. The gradual approach keeps the mixture smooth instead of curdling or seizing.

Testosterone

Testosterone is a sex hormone produced in the testes, ovaries, and adrenal glands that influences muscle mass, bone density, mood, and libido in both men and women. Levels that run too high or too low can each produce distinct symptoms, so it is worth tracking alongside other hormone labs.

Th1 (T-helper 1)

Th1, or T-helper 1, is a branch of the immune system's T-helper cells that coordinates direct, cell-based defense against threats like viruses and other intracellular invaders. Its balance with the Th2 and Th17 branches is part of how the immune system stays regulated, and shifts in that balance are studied in autoimmune disease.

Reference: The Th1/Th2 balance in autoimmunity. (Current opinion in immunology, 1995) via PubMed

Th17

Th17, or T-helper 17, is a branch of the immune response that recruits inflammatory cells to fight off fungi and bacteria at barrier tissues like the gut and skin. When Th17 activity runs high for too long, it is linked to tissue damage in several autoimmune conditions.

Reference: The pathogenicity of Th17 cells in autoimmune diseases. (Seminars in immunopathology, 2019) via PubMed

Th2 (T-helper 2)

Th2, or T-helper 2, is a branch of the immune response that directs antibody production against threats such as parasites and allergens. Its balance with Th1 and Th17 activity is part of normal immune regulation, and imbalance among these branches is studied in autoimmune and allergic conditions.

Reference: The 3 major types of innate and adaptive cell-mediated effector immunity. (The Journal of allergy and clinical immunology, 2014) via PubMed

Thai basil

Thai basil, also called horapha, is a sturdy variety of basil with a distinct licorice-anise flavor that holds up well to high heat. It is used throughout Southeast Asian cooking in stir-fries, curries, and soups.

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Thyroglobulin

Thyroglobulin is a protein made inside the thyroid gland that serves as the scaffold on which thyroid hormone is built. Because the immune system can mistakenly target this protein, antibodies against it are one of the markers checked when evaluating autoimmune thyroid disease.

Reference: Molecular Mechanisms in Autoimmune Thyroid Disease. (Cells, 2023) via PubMed

Thyroglobulin antibodies (TgAb)

Thyroglobulin antibodies, or TgAb, are immune proteins directed against thyroglobulin, the protein the thyroid uses to build its hormones. They are one of two markers commonly tested for autoimmune thyroid disease and are sometimes elevated even when TPO antibodies come back normal.

Reference: Hashimoto's thyroiditis: from pathogenesis to clinical management. (Frontiers in endocrinology, 2026) via PubMed

Thyroid

The thyroid is a small, butterfly-shaped gland at the base of the neck that produces hormones setting the pace of metabolism throughout the body. It influences energy, temperature regulation, digestion, mood, and heart rate, which is why thyroid health is central to many autoimmune recovery plans.

Thyroid antibodies

Thyroid antibodies are immune proteins that mistakenly target thyroid tissue, with TPO antibodies and thyroglobulin antibodies being the two most commonly tested. Elevated levels of either marker are used to identify autoimmune thyroid disease, often before symptoms or standard thyroid labs shift noticeably.

Thyroid binding globulin (TBG)

Thyroid binding globulin, or TBG, is a protein made in the liver that carries thyroid hormone through the bloodstream. When TBG rises, often driven by excess estrogen, more hormone stays bound and less is free to enter cells, which can produce low-thyroid symptoms despite normal total hormone levels.

Reference: Interaction of estrogen therapy and thyroid hormone replacement in postmenopausal women. (Thyroid : official journal of the American Thyroid Association, 2004) via PubMed

Thyroiditis

Thyroiditis is inflammation of the thyroid gland, which can be triggered by infection, medication, or autoimmune activity. In autoimmune forms such as Hashimoto's, the gland can swell, feel tender, or shrink over time as inflammation rises and falls.

Reference: An update on the pathogenesis of Hashimoto's thyroiditis. (Journal of endocrinological investigation, 2020) via PubMed

Tigernut

Tigernut is a small, sweet tuber that despite its name is not a nut, related instead to the sedge family of plants. Eaten as a snack or ground into flour, it provides fiber and resistant starch that can support digestive health.

Tigernut flour

Tigernut flour is a grain-free flour ground from tigernuts, small sweet tubers rather than tree nuts. It has a mild, naturally sweet flavor and is a common substitute in Autoimmune Protocol baking for those avoiding nuts and seeds.

Tight junctions

Tight junctions are the protein structures that seal the cells lining the gut wall together, controlling what is allowed to pass between them into the bloodstream. When tight junctions loosen, undigested particles and microbial fragments can slip through, a process linked to increased intestinal permeability and autoimmune activity.

Reference: Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. (Physiological reviews, 2011) via PubMed

Tinda

Tinda, also called apple gourd or Indian round gourd, is a small, round, pale green squash with mild flavor and firm flesh. It is a staple of Indian home cooking, typically simmered into curries.

See also: On the food list

Tissue transglutaminase (tTG)

Tissue transglutaminase, or tTG, is an enzyme found in the gut lining and other tissues, including the thyroid, that modifies proteins as part of normal digestion. Its structural resemblance to gliadin, a component of gluten, is central to the molecular mimicry theory linking gluten exposure to autoimmune thyroid disease.

Reference: The importance of gluten exclusion in the management of Hashimoto's thyroiditis. (Annals of agricultural and environmental medicine : AAEM, 2021) via PubMed

Tofu

Tofu is a soft, mild-tasting food made by curdling soy milk and pressing the curds into blocks, widely used as a plant protein. It is a soy product and is excluded during the elimination phase of the Autoimmune Protocol.

Tomatillo

Tomatillo is a small, tart green fruit encased in a papery husk, most familiar as the base of Mexican green salsas. It belongs to the nightshade family and is excluded during the elimination phase of the Autoimmune Protocol.

See also: On the food list

Total iron-binding capacity (TIBC)

Total iron-binding capacity, or TIBC, is a blood test measuring how much iron the blood's transport protein could carry if it were fully saturated. It is interpreted alongside serum iron and ferritin to build a fuller picture of iron status and rule out deficiency or overload.

TPO (thyroid peroxidase)

TPO, or thyroid peroxidase, is an enzyme the thyroid gland relies on to manufacture its hormones. Antibodies against this enzyme, called anti-TPO antibodies, are the most common marker used to identify Hashimoto's thyroiditis and often appear years before symptoms develop.

Reference: Thyroid peroxidase gene variants and autoimmunity in subclinical hypothyroidism: molecular mechanisms and clinical implications. (Molecular biology reports, 2025) via PubMed

Transferrin saturation

Transferrin saturation is the percentage of the blood's main iron-carrying protein, transferrin, that is currently bound to iron. It is used together with ferritin and total iron-binding capacity to help distinguish true iron deficiency from other causes of abnormal iron labs.

Transient hyperthyroidism

Transient hyperthyroidism is a temporary surge of thyroid hormone that can occur in autoimmune thyroid disease when inflammation damages thyroid tissue and releases stored hormone all at once. This spike often settles into a period of low thyroid function afterward, which is why thyroid labs can swing unexpectedly during a flare.

Triticale

Triticale is a hybrid grain bred by crossing wheat and rye to combine traits of both. It contains gluten and is excluded from the Autoimmune Protocol along with all other gluten-containing grains.

See also: On the food list

Truffle

Truffle is a rare, intensely aromatic fungus that grows underground near the roots of certain trees, prized for its earthy scent. A small amount, shaved or grated, is enough to perfume an entire dish.

Truffle oil

Truffle oil is an oil infused with truffle aroma, used in small amounts to add a rich, earthy note to finished dishes. Many commercial versions rely on synthetic flavoring rather than real truffle, so labels are worth checking.

See also: On the food list

TSH (thyroid-stimulating hormone)

TSH, or thyroid-stimulating hormone, is released by the pituitary gland to signal the thyroid to produce more hormone. It is usually the first lab ordered to screen thyroid function, though because it measures the pituitary's signal rather than the thyroid gland itself, it can miss problems that show up on other markers.

Reference: Thyroid Stimulating Hormone and Thyroid Hormones (Triiodothyronine and Thyroxine): An American Thyroid Association-Commissioned Review of Current Clinical and Laboratory Status. (Thyroid : official journal of the American Thyroid Association, 2023) via PubMed

Type 1 diabetes

Type 1 diabetes is an autoimmune condition in which the immune system destroys the insulin-producing cells of the pancreas, leaving the body unable to regulate blood sugar without external insulin. It typically develops in childhood or young adulthood and requires lifelong hormone replacement.

Reference: The immunology of type 1 diabetes. (Nature reviews. Immunology, 2024) via PubMed

Ulcerative colitis

Ulcerative colitis is a form of inflammatory bowel disease in which the immune system drives ongoing inflammation in the lining of the colon and rectum, causing cramping, urgency, and diarrhea. It runs a relapsing and remitting course and is considered distinct from Crohn's disease by the pattern and location of inflammation.

Reference: Ulcerative colitis: Recent advances in the understanding of disease pathogenesis. (F1000Research, 2020) via PubMed

Umami

Umami is the savory, deep, mouth-filling taste found in foods like mushrooms, bone broth, aged cheese, and fish sauce. It stands alongside sweet, salty, sour, and bitter as one of the basic tastes the tongue detects.

Vagus nerve

The vagus nerve is the longest cranial nerve, running from the brainstem down through the neck and chest into the abdomen, carrying signals between the gut and brain in both directions. It plays a central role in digestion, heart rate, and the body's ability to shift out of a stress response, which makes its tone relevant to gut healing.

Reference: The Gut-Brain Axis in Multiple Sclerosis. Is Its Dysfunction a Pathological Trigger or a Consequence of the Disease? (Frontiers in immunology, 2021) via PubMed

Vietnamese coriander

Vietnamese coriander, also called rau ram or laksa leaf, is a peppery, citrusy herb used fresh in Southeast Asian soups and salads. It is not related to true coriander despite the shared name.

See also: On the food list

Villi

Villi are the tiny, finger-like projections lining the small intestine that dramatically increase the surface area available for absorbing nutrients. In celiac disease, immune activity flattens these structures, which reduces nutrient absorption until the gut lining has time to heal.

Reference: Celiac disease: diagnosis and treatment. (Danish medical journal, 2015) via PubMed

Vitamin A

Vitamin A is a nutrient essential for immune signaling and for maintaining the integrity of the gut lining, skin, and mucous membranes that form the body's first line of defense. Liver and other organ meats are the richest sources, with orange vegetables providing a precursor form the body converts as needed.

Reference: Vitamin A and vitamin D regulate the microbial complexity, barrier function, and the mucosal immune responses to ensure intestinal homeostasis. (Critical reviews in biochemistry and molecular biology, 2019) via PubMed

Vitamin B12

Vitamin B12 is a nutrient required for nerve function, energy production, and the formation of red blood cells, and it is found only in animal foods. Because absorption depends on adequate stomach acid and a healthy gut lining, conditions like autoimmune gastritis or celiac disease can lead to deficiency even with sufficient dietary intake.

Reference: Autoimmune atrophic gastritis--pathogenesis, pathology and management. (Nature reviews. Gastroenterology & hepatology, 2013) via PubMed

Vitamin D

Vitamin D functions as both a vitamin and a hormone, made in the skin from sunlight exposure and playing a significant role in regulating immune cell behavior alongside its well known role in bone health. Low vitamin D status is common among people with autoimmune conditions and is an area of active research interest.

Reference: Vitamin D and immune function. (Nutrients, 2013) via PubMed

Vitamin D receptor

The vitamin D receptor is the protein inside cells that vitamin D binds to in order to carry out its effects, including switching immune-related genes on and off. Genetic variation in this receptor changes how effectively an individual's cells respond to a given vitamin D level, which is one reason lab values alone do not tell the whole story.

Reference: Vitamin D and Autoimmune Diseases: Is Vitamin D Receptor (VDR) Polymorphism the Culprit? (The Israel Medical Association journal : IMAJ, 2017) via PubMed

Vitamin K2

Vitamin K2 is a fat-soluble vitamin that helps direct calcium into bones and teeth and away from soft tissue like artery walls. It is found in animal foods and fermented foods and works alongside vitamin D in supporting bone and cardiovascular health.

Vitiligo

Vitiligo is a condition in which the immune system attacks the pigment-producing cells of the skin, leaving smooth, pale patches that can spread over time. It is considered autoimmune in origin and sometimes appears alongside other autoimmune conditions such as autoimmune thyroid disease.

Reference: Vitiligo: A Review. (Dermatology (Basel, Switzerland), 2020) via PubMed

Wakame

Wakame is a silky, dark green sea vegetable with a mild, slightly sweet flavor, most familiar as the seaweed in miso soup and seaweed salad. It is typically sold dried and rehydrated before use.

See also: On the food list

Wasabi

Wasabi is a pungent green root from Japan, related to horseradish, grated fresh or mixed from powder to make a sharp, sinus-clearing condiment. Much of what is served as wasabi outside Japan is actually colored horseradish.

Water chestnut

Water chestnut is a crisp, mildly sweet vegetable that grows submerged in water, prized in Asian cooking for the crunch it keeps even after cooking. It is often sliced into stir-fries, fillings, and salads.

See also: On the food list

Water spinach

Water spinach, also called kangkong or ong choy, is a leafy green with hollow stems that grows in warm, wet conditions. It is usually stir-fried quickly with garlic to keep its texture crisp-tender.

See also: On the food list

Whey

Whey is the liquid left over after milk curds separate during cheesemaking, containing a fast-digesting dairy protein. It is also sold as a standalone protein powder, though as a dairy derivative it stays off the Autoimmune Protocol food list.

Winter melon

Winter melon is a large, mild-flavored gourd with pale, tender flesh, used throughout Asian cooking in soups and braises. Despite the name, it is a savory vegetable rather than a sweet melon.

See also: On the food list

Yacon

Yacon is a sweet, crisp root vegetable from South America with a flavor somewhere between apple and pear, eaten raw or cooked. Much of its sweetness comes from a type of prebiotic fiber the body cannot fully digest, which can feed beneficial gut bacteria.

See also: On the food list

Yakisoba

Yakisoba is a Japanese stir-fried noodle dish traditionally made with wheat noodles, vegetables, and a savory-sweet sauce. An Autoimmune Protocol version swaps in vegetable noodles, such as those made from zucchini or cabbage, in place of wheat.

Yersinia enterocolitica

Yersinia enterocolitica is a bacterium that causes gastrointestinal infection and has been studied for its structural similarity to thyroid tissue, a resemblance researchers believe may trigger or worsen autoimmune thyroid disease in susceptible people through molecular mimicry. The exact role it plays in disease onset is still being investigated.

Reference: Identification of outer membrane porin f protein of Yersinia enterocolitica recognized by antithyrotopin receptor antibodies in Graves' disease and determination of its epitope using mass spectrometry and bioinformatics tools. (The Journal of clinical endocrinology and metabolism, 2010) via PubMed

Yuzu

Yuzu is a fragrant, tart East Asian citrus fruit valued mainly for its juice and zest rather than eaten out of hand. Its bright, floral acidity is used to brighten sauces, dressings, and marinades.

See also: On the food list

Zinc

Zinc is a mineral involved in immune cell development, repair of the gut lining, and the conversion of thyroid hormone into its active form. Oysters and red meat are among the richest sources, and low zinc status is common in people with gut or thyroid dysfunction.

Reference: Zinc Status and Autoimmunity: A Systematic Review and Meta-Analysis. (Nutrients, 2018) via PubMed

Zonulin

Zonulin is a protein the body produces that loosens the tight junctions holding gut-lining cells together, regulating how open or closed the intestinal barrier is at any given moment. Elevated zonulin activity is associated with increased intestinal permeability, a pattern researchers have linked to several autoimmune conditions.

Reference: All disease begins in the (leaky) gut: role of zonulin-mediated gut permeability in the pathogenesis of some chronic inflammatory diseases. (F1000Research, 2020) via PubMed

Zoodles

Zoodles are long, thin strands of zucchini cut to resemble noodles, typically made with a handheld or countertop spiralizer. They serve as a grain-free stand-in for pasta in Autoimmune Protocol cooking.