The Skinny on the Autoimmune Paleo Diet

Learn about the autoimmune Paleo diet. What foods are to be included and excluded when eating an autoimmune Paleo diet?

What is the Autoimmune Diet?

The now well-known Paleo diet focuses on elimination of industrial foods, sugars, and grains. There is no consensus on macronutrient ratios nor unanimous opinion about eliminated foods. The Paleo diet is open to a great deal of interpretation.

However, a segment of the diet is focused on dietary changes for those with autoimmune disease, the autoimmune Paleo diet, but called autoimmune protocol diet (AIP) in the literature. In addition to eliminating the usual suspects—grain, sugar, processed foods—the AIP also requires elimination of legumes, nightshades, dairy, eggs, coffee, alcohol, nuts and seeds, and food additives.

The rationale of this diet for autoimmunity specifically is that elimination of specific foods, dietary additives, and emulsifiers disrupt the gut flora. Several studies in inflammatory diseases suggest that interactions between dietary or bacterial metabolites and host immune cells can contribute to overall immune balance at the gut. Any disruption can affect the intestinal barrier in turn leading to dysregulation of immune cells which “recognize” potential threats, or antigens, and trigger inflammatory cells and mediators.

What’s the Deal with Nightshades?

Nightshades include tomatoes, potatoes, eggplants, sweet and hot peppers, and chili-based spices. There are zero experimental studies that examine mechanisms for which these foods are specifically inflammatory, disrupt the gut, or are immune provoking. (Prove me wrong in the comments if you can.) However, anecdotally these foods can be very problematic to those with autoimmunity. For example, eat a bell pepper and see your psoriatic rashes worsen. It remains to be seem why this is the case in some individuals. Some suggest it’s not the foods themselves but the lectin, saponin and/or capsaicin content of the food. Lectins, saponin, and capsaicin have been shown to increase intestinal permeability in some models and may worsen autoimmunity.

Autoimmune Diet for Inflammatory Bowel Disease

A 2017 study involved 15 individuals with Crohn's disease (CD) and ulcerative colitis (UC). An AIP diet was implemented for 5 weeks following a 6-week elimination diet phase. The researchers required dietary elimination of grains, legumes, nightshades, dairy, eggs, coffee, alcohol, nuts and seeds, refined/processed sugars, oils, and food additives. There was also suggested avoidance of non-steroidal anti-inflammatory drugs and low–nutrient-density processed foods.

At the end of the study, the dietary intervention either induced symptom remission or improved symptoms in 70% of the subjects with both CD and UC. However, blood marker of inflammation, CRP, did not reduce significantly. Stool marker of inflammation, fecal calprotectin, also did not significantly differ. I predict a longer duration study would see some reduction in these systemic inflammatory markers.  

Autoimmune Diet for Hashimoto’s

In 2019, a study utilized the AIP on 17 women with autoimmune thyroiditis, also known as Hashimoto’s. In concordance with the IBD study above, this AIP diet intervention also required elimination of grains, legumes, nightshades, dairy, eggs, coffee, alcohol, nuts, seeds, refined/ultra-processed sugars, oils, and food additives. Participants were advised to consume a diet rich in unsaturated fats, bone-based broth, seafood, fermented foods, and organ meats.

After a 10-week diet coaching intervention, there was statistically significant improvements in quality of life measurements. There were no changes in the women’s thyroid laboratory markers, yet maker of inflammation, CRP, reduced a whopping 29%. Perhaps a longer duration study would show significant changes in thyroid hormones and antibodies.

Both of these studies are promising. Most telling was both studies had high degrees of compliance, suggesting that these dietary changes are not insurmountable. With the exception of 2 UC patients with colon anatomical variation, no adverse effects were reported in either of these studies.

An AIP Diet is a reasonable option for those with autoimmunity. More studies will likely emerge to determine the effects of the diet on other autoimmune disorders. Here are some tips but I can work with you online to establish and monitor an AIP diet.

How to Implement the AIP Diet


Grains, Legumes, Nightshades, Dairy, Eggs, Coffee, Alcohol, Nuts and Seeds, Refined/Processed Sugars, Oils, Food Additives, Non-Steroidal Anti-inflammatory Drugs and Low–Nutrient-Density Processed Foods


Nutrient-Dense Whole Foods, Seafood, Bone-based Broths, Organ Meats, Unsaturated Fats


Eliminate all nightshades initially then reintroduce, one at a time, to detect individual food sensitivity. Repeat this process several times to validate.


Thorburn AN, Macia L, & Mackay CR (2014) Diet, Metabolites, and ‘‘Western-Lifestyle’’ Inflammatory Diseases. Immunity. 40(6):833-42.

Gee JM, et al (1996) Effects of saponins and glycoalkaloids on the permeability and viability of mammalian intestinal cells and on the integrity of tissue preparations in vitro. Toxicol In Vitro. 10(2):117-28.

Konijeti GG et al. (2017) Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 23(11):2054-2060.

Abbott R D, Sadowski A, Alt A G (2019) Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. Cureus 11(4): e4556. doi:10.7759/cureus.4556 .