Diet and Autoimmunity

Autoimmune disorders are more common today than ever in the recorded past, and 80+ types of autoimmune diseases have been identified1. Autoimmunity is part of the immune system’s natural way of protecting itself, and plays a major role in wellness2. Still, every human possesses the potential to trigger an autoimmune disease (when the same autoantibodies that normally combat disease end up attack themselves1,3).

Scientists recently studying the causes of Celiac disease – an autoimmune condition related to gluten proteins – discovered the “Holy Trinity” of susceptibility to developing autoimmunity: genetic predisposition, a trigger, and leaky gut4. In other words, three factors must occur in tandem in order for autoimmunity to develop.

An individual may possess two factors, for example 1.) genetic risk for Celiac disease and 2.) a dietary trigger, gluten. But if this person’s gastrointestinal tract is high functioning and properly “trafficking” which substances pass into the bloodstream, then it’s less likely for autoimmunity to develop at that time. If the gut is compromised, then antigens (toxins, bacterial or fungal microorganisms, tumor cells, and more – either from the external environment or inside the body) pass through the intestinal lining and provoke the immune system to release antibodies to attack these particles now seen as invasive. There are innumerable antigens inherently present in the human body; red blood cells alone contain over 400 antigens.3

Still, less than 10 percent of individuals genetically susceptible to disease will actually develop the at-risk disease5, suggesting that environmental triggers play a huge role in autoimmunity. Toxins (widespread in food, soil, air, water, household and beauty products, building materials, furniture, etc.), food allergens, medications (many compromise the single layer of cells lining the gut), and infections6 cause inflammation and hypersensitivity of the gut. These factors may become triggers of disease and contribute to increased intestinal permeability. Chronic exposure explains why many people develop autoimmunity over time and later in life.

We cannot change our genes, however dietary changes can help alleviate two components of The Holy Trinity: triggers related to food consumption and a compromised gastrointestinal tract.

The aim of the Autoimmune Protocol (AIP) is to remove typical gut-destructive foods and consume only immune-supportive foods. The AIP is basically a strict elimination diet: exclude foods high in toxins that disrupt hormone, gut and immune function and impair cellular integrity, such as potentially-allergenic eggs, dairy, grains, legumes, nuts; most sugars; vegetable oils; dyes, preservatives, antibiotics, GMOs and artificial everything.

Basically, the AIP returns to ancestral foods, such as pasture-raised or wild meat and fish, organ meats (yep, liver!), and whole, nutrient-dense foods prepared from scratch. Often pegged as a limited Paleo diet, the AIP is tailored to the individual. For example, meat and fish consumption may account for only 10-15% of the diet, while vegetables, herbs, some fruits, certain oils and fermented foods may make up the other 85-90%. These healing foods reduce inflammation, stimulate the immune system and restore intestinal gut lining. When optimal physiologic function has been restored, many people find they may add back properly prepared, high-quality foods from the restricted list1.

While autoimmunity may never heal completely, it may be sent into remission by addressing healing factors through the removal of environmental exposures, lifestyle changes and a toxin-free, nutrient-dense diet. The Autoimmune Protocol may not be appropriate for every person or condition. Please consult with a health practitioner trained in clinical functional nutrition before embarking on an AIP journey.



1Flanigan, J. (n.d.). What is autoimmune paleo or AIP diet? AIP lifestyle. Retrieved from

2Lleo, A., Invernizzi, P., Gao, B., Podda, M. & Gershwin, M.E. (2010). Definition of human autoimmunity--autoantibodies versus autoimmune disease. Autoimmune Review; 9(5):A259-66. doi: 10.1016/j.autrev.2009.12.002. Epub 2009 Dec 4.

3Fischbach, F.T. (2003). Manual of laboratory and diagnostic tests (7th ed.). Lippincott Williams & Wilkins Publishers.

4Fasano, A. (2011). Zonulin and Its Regulation of Intestinal Barrier Function: The Biological Door to Inflammation, Autoimmunity, and Cancer. Physiological Reviews91(1), 151–175.

5Fasano, A. (2012). Intestinal Permeability and its Regulation by Zonulin: Diagnostic and Therapeutic Implications. Clinical Gastroenterology and Hepatology: The Official Clinical Practice Journal of the American Gastroenterological Association10(10), 1096–1100.

6Menard, S., Cerf-Bensussan, N., Heyman, M. (2010). Multiple facets of intestinal permeability and epithelial handling of dietary antigens. Mucosal Immunology: 3(3).

What is autoimmunity? (n.d.). Johns Hopkins Medical Institutions: Autoimmune Disease Research Center. Retrieved from