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All About: The Autoimmune Protocol Diet

The Autoimmune Protocol diet is popular among people with AI conditions and allergies. How effective is this diet? What does the research say?

Key Points

  • There are meaningful benefits from the diet for inflammatory bowel conditions
  • There are also possible benefits for Hashimoto’s thyroiditis
  • Studies performed thus far have not been randomised, placebo-controlled studies
  • We cannot rule out that less restrictive, healthy diets could result in similar benefits
  • Note: I have seen in clinical practice that less-restrictive diets have been very effective for my patients with autoimmune conditions

The autoimmune protocol diet (AIP) is a variant of the popular ‘Paleo’ diet in which common irritants and allergens that are suspected of being triggers for autoimmune reactions in the body or that cause intestinal inflammation and a ‘leaky gut’, are also eliminated. It is designed mostly for people with autoimmune conditions such as psoriasis, Hashimoto’s thyroiditis (the most common cause of hypothyroidism), Crohn’s disease, ulcerative colitis, rheumatoid arthritis, and lupus (amongst others).

Autoimmune conditions are ones in which the body launches immune attacks against self-tissue or against resident microbes on or within that tissue, creating primary damage and secondary damage through increased inflammation and oxidation. Many factors are linked to autoimmune conditions including genetic predisposition and dietary and lifestyle triggers.

The body launches immune attacks against self-tissue

 In a ‘leaky gut’ increased intestinal permeability leads to the entry into the body of larger molecules (than are usually absorbed) and these can be mistakenly identified as pathogens, leading to immune dysfunction. Leaky gut is intricately tied to the health of the microbiome and gut-health in general and increased intestinal permeability may result from a diet that is excessively high in sugar, low in nutrients such as zinc and omega-3 fatty acids, and resultant ‘dysbiosis’ (distorted microbe levels in the gut) resulting from poor diet and lifestyle habits (along with genetic components).

The Autoimmune Protocol Diet

Allowed foods Disallowed foods
Meat and fish (preferably not factory raised)
Vegetables (but not nightshades, such as tomatoes, eggplants, peppers, and potatoes)
Sweet potatoes
Fruit (in small quantities)
Coconut milk
Avocado, olive, and coconut oil
Dairy-free fermented foods, such as kombucha, kefir made with coconut milk, sauerkraut, and kimchi
Honey or maple syrup (but only to be used occasionally, in small quantities)
Fresh non-seed herbs, such as basil, mint, and oregano
Green tea and non-seed herbal teas
Bone broth
Vinegars, such as apple cider and balsamic
All grains (such as oats, rice, and wheat)
All dairy
Legumes (such as beans and peanuts)
Nightshade vegetables (tomatoes, eggplants, peppers, and potatoes)
All sugars, including sugar replacements (except for occasional use of honey)
Butter and ghee
All oils (except for avocado, coconut, and olive)
Food additives

Does it work?

Inflammatory bowel disease

An uncontrolled 11-week study in four patients with ulcerative colitis showed changes to gene expression related to reduced T-cell mediated inflammation and promotion of intestinal mucosal healing along with clinically relevant remission.1 In a similar study on 15 patients with inflammatory bowel disease (ulcerative colitis and Crohn’s disease), faecal calprotectin (a measure of intestinal inflammation and disease activity) improved from 471 (± 562) to 112 (± 104) by week 11 (p = 0.12). Among those receiving a post-study endoscopy (n = 7) there were improvements in disease activity observed in 4 of these.2 Improvements in bowel frequency, sports performance,3 reduced steroid use, successful reintroduction of foods over time,4 and overall quality of life,5 have also been observed in people with IBD following an AIP.

Hashimoto’s thyroiditis

In Hashimoto’s thyroiditis, both symptoms profile and overall health were observed to improve with the AIP, along with decreased inflammation (as measured by c-reactive protein), but there were no significant changes in thyroid hormones or antibodies.6


So, there do seem to be meaningful benefits from the AIP diet for IBDs and possibly also for thyroiditis, but the studies performed thus far have not been randomised, placebo-controlled studies, and we cannot rule out that less restrictive, healthy diets could result in similar benefits.

I have seen in clinical practice that less-restrictive diets have been very effective for my patients with autoimmune conditions. In the case of the study on thyroiditis it is also significant that there were no meaningful reductions observed for thyroid hormones or antibodies and so, it would be cavalier for anyone to think that an AIP diet could ‘cure’ their thyroiditis and it is important to continue medications or other treatments and to continue to have thyroid hormones and antibodies monitored under the guidance of a physician and other appropriately qualified health practitioners.

Less-restrictive diets have been very effective for my patients with autoimmune conditions


1.            Konijeti G, Molparia B, Akhtar E, Wang X, Chang J, Lewis J, et al. P539 Transcriptional changes in mucosal inflammation associated with an autoimmune protocol diet for ulcerative colitis. Journal of Crohn’s and Colitis. 2018;12(supplement_1):S378-S.

2.            Konijeti GG, Kim N, Lewis JD, Groven S, Chandrasekaran A, Grandhe S, et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflammatory Bowel Diseases. 2017;23(11):2054-60.

3.            Groven S, Sanchez C, Levy S, Lewis JD, Caroline D, Singh E, et al. Rapid Improvement in Symptoms and Quality of Life among Patients with Inflammatory Bowel Disease following an Autoimmune Protocol Diet. Gastroenterology. 2017;152(5):S410.

4.            Lee J, Konijeti G, Pedretti C. Clinical Course and Dietary Patterns Among Patients Incorporating the Autoimmune Protocol for Management of Inflammatory Bowel Disease (P12-010-19). Current Developments in Nutrition. 2019;3(Supplement_1).

5.            Chandrasekaran A, Groven S, Lewis JD, Levy SS, Diamant C, Singh E, et al. An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease. Crohn’s & Colitis 360. 2019.

6.            Abbott RD, Sadowski A, Alt AG. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. 2019.

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