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Autoimmune Paleo Diet and Autoimmune Disease - The Facts

by Rahul Kapur

Autoimmune Paleo Diet and Autoimmune Disease - The Facts

If you are one of the tens of millions of Americans who suffer autoimmune disease, you’ve probably heard of the Autoimmune Protocol diet. 

An  extension of the Paleolithic Diet, the “AIP” diet  advises eliminating foods and medications known to cause intestinal inflammation, dysbiosis and food allergies and then reintroducing them one at a time to determine which may be causing symptoms. Typically, dieters eliminate  grains, legumes, nightshades, dairy, eggs, coffee, alcohol, nuts and seeds, refined/processed sugars, oils, and food additives over a six-week period. These items are replaced with fresh, nutrient-dense foods such as bone broth, as well as fermented foods.

The premise is that autoimmune disease (AID) is caused when toxins, antigens and bacteria leak through the one-cell layer separating your digestive tract from the rest of your body. There is growing evidence that dysbiosis, or an imbalance of gut bacteria needed to digest much of what we eat, is among the factors that can cause, or worsen, leaky gut.  

Like makers of probiotics, proponents of the diet claim it can help prevent or correct dysbiosis and AID by resetting the immune system. But does the AIP diet really work? 

Growing evidence from human and animal research suggest that it can help relieve AID symptoms and even bring about remission. Moreover, because there are no known cures for AID and existing therapies have many adverse side effects, doctors have increasingly been prescribing the AIP diet as part of broader lifestyle interventions to help patients manage their symptoms. 

Promising Clinical Trials

Early clinical trials have shown promising results. Since 2016, AID patients participating in two lifestyle intervention programs involving the AIP diet have reported significant relief from their symptoms. 

After just 10 weeks, 16 women enrolled in one such program reported significant relief from symptoms of Hashimoto’s thyroiditis (1), the most common cause of hypothyroidism in the United States. While there were no statistically significant changes noted in their thyroid function or thyroid antibodies, they reported relief from their symptoms. In some instances, endoscopies and tests for proteins and blood cells showed less inflammation. The study’s findings suggest that AIP may decrease systemic inflammation and modulate the immune system, the authors wrote. 

A 2017 study that followed nine patients suffering from Crohn’s Disease and six suffering from ulcerative colitis through an 11-week program found the AIP significantly improved clinical symptoms and quality of life of patients within the first three weeks. (2)

The diet consisted of a 6-week elimination phase followed by a 5-week maintenance phase during which no food groups could be reintroduced. Patients were provided two books on AIP diet and recipes, access to a life coach and nutritionist and an online support group. 

By week six, 11 of the 15 patients had achieved clinical remission, which they sustained through the remainder of the program. Patients reported more frequent bowel movements, feeling less tense and participating in more leisure and sports activities, but did not report feeling less fatigue or irritability or fewer abdominal cramps. Blood and other tests, meanwhile, did not reveal statistically significant changes in AID biomarkers, or proteins and blood cells that signal inflammation. 

While encouraging, it should be noted that the studies were extremely small and did not control for many factors that are also known to contribute to AID. Seven of the inflammatory bowel disease (IBD) patients, for instance, were undergoing biologic therapy for their condition during the program. Controlling for such factors remains a significant obstacle to conducting large scale research on AID.

The Western Diet, Obesity and AID

Regardless, U.S. doctors are increasingly incorporating diet into their treatment due to a growing body of research linking the high fat, salt and sugar content of the Western Diet to obesity and metabolic syndrome, which are the most consistent predisposing factors across a large set of inflammatory autoimmune diseases. 

Obesity is essentially an excess of adipose, or fat tissue, which secretes a wide variety of “adipokines,” or hormones,  that have both pro- and anti-inflammatory effects. Adipokines have been shown to play a role in triggering IBD as well as other AIDs, such as rheumatoid arthritis, psoriasis , type 1 diabetes and multiple sclerosis. 

The percent of U.S. adults considered obese grew more than 2.5 times to nearly 40 percent from 1980 to 2016, during which time AID emerged as a leading cause of death among young and middle-aged women in the United States, according to a 2011 review of prior research studies. (4) The study identified 120 AIDs, up from the 80 thought to exist at the time. 

Genetics are unlikely to change fast enough to trigger such a rapid increase, so some researchers suspect environmental factors, including diet and lack of exercise, are contributing to the rapid spread of AID. 

This theory has been boosted by studies showing that it is possible for one identical twin to develop psoriasis and other AIDs, while the other does not. 

By 2016, the National Institutes of Health estimated AID affected more than 23.5 million people in the United States. 

The most obvious evidence of food triggering AID is found in celiac disease, which attacks the small intestine. Remove gluten from the diet and the symptoms disappear.

Maintaining a healthy body weight, consuming a healthy diet, not smoking, and exercising at least 150 minutes a week is related to a substantially lower risk of developing gestational diabetes, according to an NIH analysis of data from a long-term study that included more than 10,000 women.(5) Women at low risk for all four factors had more than 80 percent less risk of gestational diabetes. A combination of the four risk factors may account for nearly half of all cases of gestational diabetes, the study concluded. 

Frequent consumption of soybean drinks may help protect against androgenic alopecia, according to one Chinese study. A 2019 review of 55 closely vetted studies of lupus  patients concluded diet can promote their body's homeostasis, increase their time in remission, prevent adverse effects of medication and improve their physical and mental well-being. 

A long-term study of the elderly in Baltimore has showed that higher adiposity at midlife is associated with more neurofibrillary tangles in the brain and accelerates the onset of Alzheimer’s Disease. This  suggests maintaining a healthy body mass index in your 50s could delay the onset of AD symptoms decades later. 

Some scientists have recently begun to consider the possibility that Alzheimer’s disease is, in fact, an autoimmune disease.

Microbiomes and Autoimmune disease

Research funded by the NIH has discovered that the gut microbiota plays an important role in preventing adults from developing autoimmune and inflammatory diseases in the skin. One study of psoriasis using mice found that the gut microbiota in early life contribute significantly to health of an adult, and the uncontrolled use of antibiotics, especially in childhood, may increase susceptibility to autoimmune disease and inflammation in adults.  

A separate NIH-funded study found that the bacterium Prevotella copri (P. copri) was more abundant in patients with new-onset, untreated rheumatoid arthritis than in healthy patients, patients with rheumatoid arthritis who were receiving treatment, and patients with psoriatic arthritis. While more extensive studies are needed, the findings suggest the bacterium contributes to the development of the disease.

Regardless of your health, there are plenty of reasons to reduce your intake of foods that can contribute to dysbiosis, obesity, hypertension, DIA and other diseases. Abundant research has shown that high consumption of processed foods, which can contain up to 100 times more salt than home prepared foods, can lead to an array of chronic illnesses. In a 2018 study, 84 percent of stool samples taken from people who had eaten a Western diet tested positive for the fungus Candida, which may contribute to IBD. That compared to 64 percent of stool samples taken from test subjects on vegetarian diets. (6)

But before you embark on the AIP diet, remember that the patients participating in the AIP diet studies described above were screened and monitored throughout the process by a multidisciplinary clinical team. Indeed, the one IBD patient to experience an adverse effect was admitted to the hospital for partial small bowel obstruction three weeks after starting the diet. It turns out she had not communicated with her health coach or dietician about a known stricture in her bowels before significantly increasing her consumption of raw vegetables, salad and meat. 

So please, if you suffer from AID, consult your doctor before making any dietary changes. 


PLEASE NOTE that this article is not in lieu of medical advice from your doctor. All content found on this website including: articles, text, images, audio, videos, or other formats were created for informational purposes only.  This content is not intended to be a substitute for professional medical advice, diagnosis, or treatment.


Additional resources:

American Autoimmune Related Diseases Association Inc. is dedicated to the eradication of autoimmune diseases and the alleviation of suffering and the socioeconomic impact of autoimmunity through fostering and facilitating collaboration in the areas of education, public awareness, research, and patient services in an effective, ethical, and efficient manner.

The Paleo Approach: Reverse Autoimmune Disease and Health Your Body,” by Sarah Ballantyne, 2014, Victory Belt Publishing. One of two cookbooks provided IBD patients participating in a clinical trial described in a 2017 study. See Footnote 3 

The Autoimmune Paleo Cookbook: An Allergan-Free Approach to Managing Chronic Illness,” by Mickey Trescott, 2014, Trescott LLC. One of two cookbooks provided IBD patients participating in a clinical trial described in a 2017 study. See Footnote 3

  1. Abbot, RD, Sadowski AG. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis. Cureus, April 27, 2019,   https://assets.cureus.com/uploads/original_article/pdf/18455/1556644567-20190430-9065-ltx44s.pdf
  2. Konijeti GG, Kim N, et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflammatory Bowel Diseases, Nov. 23, 2017  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647120/#__ffn_sectitle
  3. Manzel A, Muller DN, Hafler DA et al. Role of “Western Diet” in Inflammatory Autoimmune Diseases. Curr Allergy and Asthma Reports, Jan 10, 2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034518/pdf/nihms549353.pdf
  4. Schmidt CW. Questions Persist: Environmental Factors in Autoimmune Disease. Environmental Health Perspectives, July 2011 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114837/
  5. Report of the Director, National Institutes of Health, Fiscal years 2014 and 2015. Page 192 

Rahul Kapur
Rahul Kapur