Autoimmune Protocol Diet, Simplified.

by Rachel Stuck, RDN

What is autoimmune protocol (AIP)?

Autoimmune protocol (AIP) is an elimination diet recommended primarily to individuals who have autoimmune diseases. The goal of the diet is to reduce inflammation and relieve symptoms of autoimmune disorders. AIP will not cure autoimmune diseases or replace medications.

AIP resembles a paleo-style diet with a few small differences related to the types of vegetables included and the short-term elimination of eggs, nuts, and seeds. There are three main phases of the AIP diet: the elimination phase, the maintenance phase, and the reintroduction phase. During the elimination phase, certain foods are avoided for at least 30 days. Most health professionals recommend a 60- to 90-day maintenance phase following the initial 30-day elimination period. Although it is the most straightforward, the maintenance phase can be the toughest phase. It requires planning, carefully choosing the foods you eat, and a little extra willpower. During the reintroduction phase, foods are slowly reintroduced one at a time to assess for adverse reactions.1
  • Phase 1: Elimination – (at least 30 days) eliminate all foods that are not AIP-compliant
  • Phase 2: Maintenance – (minimum of 30 days) best results when followed for 60–90 days
  • Phase 3: Reintroduction – slowly reintroduce one food a week and assess for symptoms

Before starting any new diet or protocol, check with your physician. AIP should only be completed under the guidance of a doctor, registered dietitian, nutritionist, or other trusted health professional.

Who should consider AIP?

Individuals who have been diagnosed with autoimmune diseases—specifically, those who are struggling to manage their symptoms and maintain daily activities—may benefit from AIP. 2 Individuals who suspect they have an autoimmune disease may also benefit from the AIP diet, but should seek guidance from a health professional before making dietary changes.

Autoimmune diseases that may benefit from AIP:

  • Inflammatory bowel disease (IBD)
    • Crohn’s disease (CD)
    • Ulcerative colitis (UC)
  • Celiac disease
  • Fibromyalgia
  • Graves’ disease
  • Hashimoto’s thyroiditis
  • Multiple sclerosis
  • Psoriasis
  • Rheumatoid arthritis (RA)
  • Type 1 diabetes
  • Other autoimmune diseases

AIP and Gut Health

The gut plays a key role in the symptoms and management of autoimmune diseases.3 The population and diversity of the gut microbiome has been found to differ between individuals with autoimmune disease and the healthy controls.4 Scientists are working to understand whether an imbalanced gut microbiome, also called dysbiosis, triggers the autoimmune response or if the autoimmune disease creates a dysbiosis.5 Dysbiosis can cause the intestinal barrier to break down, which increases the risk of pathogens (bacteria and viruses) entering the bloodstream and causing an immune response.

The intestinal wall breakdown also creates heightened food sensitivity and intestinal permeability, also called “leaky gut.” Research shows that most autoimmune conditions share a common underlying problem: a more permeable or “leaky” intestinal lining.

The goal of AIP is to heal the intestinal lining by relieving the gut of common irritants. During the elimination and maintenance phase, the gut is able to heal itself and rebuild a more diverse and well populated gut microbiome. Then, when the reintroduction phase begins, the gut may be able to tolerate foods it could not tolerate in the past. With that said, the AIP diet may need to be completed more than once if symptoms related to poor diet and lifestyle choices or stress begin to flare up again.

More Than a Diet

The elimination phase of AIP is the foundation of the AIP protocol, but many who recommend AIP also recommend assessing lifestyle habits as well. Sleep health, emotional well-being, stress management, regular exercise, and mindfulness practices are often key components of a successful AIP protocol. If you are considering starting AIP to manage autoimmune symptoms and heal your gut, it is important to also assess practices outside of your diet.

Review the articles below for support on simple lifestyle habits that make a big impact on your gut health and overall wellness.

How to Get Started

Few people are able to decide to do the AIP diet one day and then get started the next. AIP takes preparation, family and community support, and dedication. Before starting the AIP, review the list of tips and recommendations below.

  1. Talk to your physician about the AIP diet and ask if they will support you in completing the 60–90 day elimination phase.
  2. Talk to your family and friends about why you are going to be completing AIP, and ask them for support.
  3. Do your research. Get familiar with AIP and identify which foods you can eat and which you are going to avoid. Then, draft a few meals and snacks that will be AIP-compliant and, most importantly, satisfying.
  4. Start meal prepping. Meal prep and batch cooking will help to keep you on track on days when you’re feeling tempted by foods that are not AIP-compliant. Having a variety of prepared foods on hand will make life easier and take the guesswork out of mealtime. If you can prepare a few meals and load up on AIP-compliant ingredients before getting started, your transition into the first phase will be much more successful.
  5. Avoid starting AIP around holidays or special occasions. These events make it even more challenging to complete the elimination phase.
  6. Be prepared to go all in. Instead of starting with 1 or 2 foods, complete elimination is recommended, especially if you are attempting to reduce symptoms related to an autoimmune disease. To get the full benefit from the AIP diet, do your best to follow the complete diet for at least 30 days.
  7. Build a support system. There are many online and in-person groups to support people who are following AIP. This is a great way to learn tips and tricks for getting through the toughest days. A dietitian, nutritionist, or health professional will also be a supporter and guide through each phase of the diet.

Additional Resources from Research-Based Organizations:


  1. Fletcher, Jenna. “AIP Diet: What Is It and What Can You Eat?” Medical News Today, MediLexicon International, 3 Jan. 2020,
  2. Abbott, Robert D, et al. “Efficacy of the Autoimmune Protocol Diet as Part of a Multi-Disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis.” Cureus, Cureus, 27 Apr. 2019,
  3. Loria, Keith. “Common Gut Bacteria Linked to Autoimmune Diseases.” Managed Healthcare Executive, 1 Feb. 2019,
  4. Huff, Gloria. “Gut Bacteria May Hold Key to Treating Autoimmune Disease.” Research Features, 31 May 2018,
  5. Yale University. "The enemy within: Gut bacteria drive autoimmune disease." ScienceDaily. ScienceDaily, 8 March 2018,