Autoimmune Protocol Diet

An extension of the Paleo diet

Reviews in the medical literature describe the Autoimmune Protocol (AIP) as an extension of the Paleolithic diet that adds a further layer of food elimination. A 2017 pilot study from Scripps Clinic in inflammatory bowel disease states that its participants received two books before starting: The Paleo Approach by Sarah Ballantyne and The Autoimmune Paleo Cookbook by Mickey Trescott, both dated 2014 in the study's reference list.

A 2024 review places the appearance of the AIP, together with the separate Wahls protocol for multiple sclerosis, within roughly the preceding decade. The same review traces elimination diets in general to older practice, naming gluten removal in celiac disease and the low-FODMAP diet of the early 2000s as earlier iterations. Its brief historical statements are second-hand and were not checked against historical scholarship for this page. The sources reviewed do not document the earliest public use of the AIP before the 2014 books.

The stated rationale

Advocates and reviewers describe the AIP as premised on the idea that food antigens cross a dysfunctional gut barrier, sometimes called increased intestinal permeability or leaky gut, and may then provoke immune responses. The review that sets out this rationale also cautions that describing gut microbes as simply good or bad is misleading. The Scripps study adds that the AIP includes dietary changes previously studied in inflammatory bowel disease, such as avoiding gluten and refined sugar. This rationale is a hypothesis held by proponents and not a finding of the trials described later.

Names in use

The practice is called the Autoimmune Protocol, the AIP diet or the Autoimmune Protocol Diet, and early books used the phrase autoimmune Paleo. One review describes it as a personalized elimination diet, meaning that foods are removed and then returned one at a time so that a person can identify which ones seem to provoke symptoms. Wahls protocol is a separate named diet for multiple sclerosis and is not covered on this page.

Relation to similar diets

The 2024 review distinguishes the AIP from the Paleo Diet: the Paleo diet follows one fixed pattern for everyone, whereas the AIP removes more foods during its first phase and then tailors the long-term pattern to individual responses. Other Machipedia pages cover related approaches, including Dietary Approaches (the family this page belongs to), Anti-Inflammatory Diet and Gluten-Free Diet. A 2026 narrative review of dietary interventions in inflammatory bowel disease lists the AIP alongside the anti-inflammatory, low-FODMAP and Mediterranean diets as separate named interventions.

Three phases

Published descriptions divide the AIP into an elimination phase, a reintroduction phase and a maintenance phase. In the elimination phase several groups of foods, additives and substances are removed. Reviewers report elimination lasting from about six weeks to six months, and the Scripps trials used a six-week elimination phase followed by a five-week maintenance phase. In the reintroduction phase, removed items are returned in sequence to see which are tolerated, and the maintenance phase has no fixed length. This page gives no food lists or plans.

Support and lifestyle components

Reviewers state that carrying out the AIP correctly needs guidance on how long to eliminate, when to reintroduce and how to sequence new items. One Hashimoto's study delivered it as a 10-week online coaching program that also addressed sleep, stress and movement, so the diet was not the only component. A second review notes that reintroduction is difficult to interpret during a flare of disease, which is why the approach is described as suited to periods of stability.

What proponents hold

Proponents present the AIP as a way to reduce inflammation, support gut health and ease symptoms of autoimmune conditions, and to help a person identify personal food triggers. Published research has focused on inflammatory bowel disease, Hashimoto's thyroiditis and rheumatoid arthritis. One review also lists eczema, migraine, eosinophilic esophagitis and attention deficit hyperactivity disorder as other conditions for which the diet has been suggested, and describes the supporting evidence there as low.

Limits of the claims

None of the sources reviewed shows that the diet reverses or removes an autoimmune disease. The studies described below measured symptoms, quality of life or short-term laboratory markers rather than long-term disease course, and one review calls the whole body of research too underpowered and subjective to support strong conclusions about benefit.

Inflammatory bowel disease

The best-known study is an uncontrolled pilot of 15 adults with active Crohn's disease or ulcerative colitis who followed the AIP for 11 weeks. Mean disease scores fell: the partial Mayo score in ulcerative colitis went from 5.8 to 1.0 and the Harvey-Bradshaw index in Crohn's disease from 7 to 3.4. C-reactive protein did not change significantly, fecal calprotectin fell without reaching statistical significance, and only 7 participants had follow-up endoscopy.

A report on the same cohort found improved self-reported quality of life, with a mean short IBD questionnaire score rising from 46.5 to 60.5 by week 11. A 2024 systematic review of dietary treatment in adults concluded that evidence for specific diets, the AIP among them, is limited. A 2026 narrative review states that the AIP did not significantly improve quality of life, a difference from the cohort report that this page cannot resolve.

Hashimoto's thyroiditis and rheumatoid arthritis

A 2019 pilot enrolled 17 women with Hashimoto's thyroiditis in a 10-week online coaching program built around the AIP, and 16 completed it. Self-reported quality of life and symptom scores improved, and high-sensitivity C-reactive protein fell by 29 percent, but thyroid hormones and thyroid antibodies did not change significantly. There was no control group. A 2024 review reports a second uncontrolled Hashimoto's study and a non-randomized crossover trial in rheumatoid arthritis that reported improved fatigue, pain and sleep, and calls all of these studies underpowered and reliant on subjective measures.

A separate 2021 review examined gluten exclusion in Hashimoto's thyroiditis, not the AIP as a whole. It found few, limited studies with ambiguous results and did not support advising gluten elimination.

Searches and what remains unknown

For this page PubMed was searched for the autoimmune protocol diet, for the Scripps IBD investigators, and for Hashimoto's and Paleo elimination studies. The studies and reviews found describe small uncontrolled or non-randomized studies, and no large randomized trial of the AIP was identified among them. Trial registries were not searched. Reviewers note no long-term data on the maintenance phase.

Positions of gastroenterology and rheumatology sources

The American Gastroenterological Association's 2024 clinical practice update on diet in inflammatory bowel disease is an expert review without formal grading of evidence. It advises a Mediterranean-style diet unless contraindicated, states that no diet has consistently reduced flares in adults, warns that restriction can contribute to malnutrition, and calls registered dietitians essential. Its abstract does not name the AIP.

A 2023 review by a rheumatologist and a nutrition scientist concluded that nutrition therapy in rheumatoid arthritis should be an adjunct to medical treatment, based on a Mediterranean diet, and urged closer work between rheumatologists and registered dietitians. No statement on the AIP itself was found from a rheumatology, gastroenterology or dietetic body, so these are general positions on diet.

Nutritional adequacy and physical harms

The reviewed trials did not measure nutrient intake systematically, but they report signals. In the Hashimoto's study, about half of participants had folate, vitamin B or riboflavin deficiencies, some present before the diet began. The Scripps pilot started vitamin D and iron repletion for deficiencies found in participants. A review warns that prolonged time in the elimination phase carries risk of deficiency and malnutrition, and the AGA update links dietary restriction in inflammatory bowel disease to malnutrition.

Adverse events in the IBD pilot included one participant with a prior ileal stricture who was hospitalized with a partial small-bowel obstruction after high intake of raw vegetables, and another whose symptoms worsened and who withdrew. Reviewers advise against the AIP in people with ileal strictures or malabsorption and report that some people experience headache, fatigue or irritability when starting. Weight and body-fat loss occurred in some trials.

Psychological and social burden

A review states that people with eating disorders, or who are prone to orthorexia, may find the restrictive structure potentially triggering, and that following the diet can bring feelings of social isolation. An Italian case-control study of 113 patients with inflammatory bowel disease and 45 controls used a screening questionnaire and classed 77 percent of patients as at risk for orthorexia nervosa against 47 percent of controls. This was a screening of food beliefs in inflammatory bowel disease generally, not of AIP followers, and a screening score is not a diagnosis.

Suitability, training and care boundaries

The sources describe no evidence that the AIP replaces conventional treatment; in the Scripps pilot, 7 of 15 participants were taking biologic drugs, and reviewers describe the AIP as a possible adjunct needing individual guidance. Medical treatment of an autoimmune condition should not be stopped or delayed because of a diet. Pregnant and breastfeeding people, children, and people with a history of disordered eating are groups for whom reviewers report a lack of evidence or a specific caution.

No AIP-specific certification from a dietetic professional body was found. In the United States, the Registered Dietitian Nutritionist title requires at least a graduate degree from an accredited program, supervised practice and a national examination administered through the Commission on Dietetic Registration. Dietitians are the professionals that gastroenterology reviews name for managing complex or restrictive diets; see Dietetics and Nutritional Therapy for how those fields are organized.