What is the origin of the autoimmune protocol diet?

October 30, 2025 •

3 min read

The autoimmune protocol (AIP) diet, developed around 20 years ago, is an intentional, phased dietary approach aimed at managing autoimmune conditions. The diet's origin is closely tied to the Paleolithic diet movement and the emerging understanding of gut health's link to systemic inflammation.

Quick Summary

The Autoimmune Protocol (AIP) diet is a therapeutic strategy that originated from Paleo principles established by Dr. Loren Cordain and was later refined by Dr. Sarah Ballantyne into a systematic, research-backed protocol.

Key Points

Paleo Diet Origin: The Autoimmune Protocol (AIP) diet emerged as a stricter version of the Paleo diet, building on its core principles.
Influenced by Loren Cordain: Dr. Loren Cordain's work on the Paleo diet established the idea that modern foods could cause inflammatory responses in people with autoimmune disease.
Refined by Sarah Ballantyne: Medical biophysicist Dr. Sarah Ballantyne, through extensive research and her book The Paleo Approach, refined the concept into the systematic, therapeutic AIP protocol.
Gut Health Focus: The foundational theory of AIP centers on healing gut permeability, or "leaky gut," to reduce the inflammatory immune response.
Phased Elimination: The protocol operates in distinct elimination and reintroduction phases to help individuals identify and manage their specific food triggers.
Research Supported: Small-scale clinical trials have demonstrated that AIP may improve symptoms and quality of life for certain autoimmune conditions like IBD and Hashimoto's.

The Roots in the Paleo Movement

The story of the autoimmune protocol (AIP) diet begins with the broader Paleolithic or Paleo diet movement, which gained significant traction in the early 2000s. The Paleo diet, based on the eating habits of ancient hunter-gatherers, emphasizes whole, unprocessed foods and restricts grains, legumes, dairy, and refined sugars. It was proponents like Dr. Loren Cordain, a founder of the Paleo movement, who first theorized that certain modern foods could trigger inflammation in genetically susceptible individuals, including those with autoimmune diseases.

This early connection between diet, inflammation, and autoimmune disorders laid the critical groundwork for a more targeted dietary intervention.

The Refinement by Dr. Sarah Ballantyne

While Cordain provided the initial inspiration, the AIP diet as it is known today was systematized and widely popularized by Dr. Sarah Ballantyne. Ballantyne leveraged her scientific background and personal experience to transform the Paleo concept into a structured protocol. Her research focused on the connection between diet, gut permeability, and the immune system. She expanded the list of restricted foods beyond Paleo guidelines to include other common triggers like eggs, nightshade vegetables, nuts, and seeds. Her 2013 book, The Paleo Approach, became a key guide, outlining a phased approach for managing autoimmune disease.

The Scientific Rationale: Gut Permeability and Inflammation

The science behind AIP centers on the theory of increased intestinal permeability, or "leaky gut". When the intestinal lining is compromised, it can allow particles into the bloodstream, triggering an inflammatory immune response that may worsen autoimmune symptoms.

The AIP protocol aims to address this by removing potential irritants, providing nutrient-dense foods to support gut healing, and promoting a healthy gut microbiome. This approach seeks to reduce inflammation and mitigate autoimmune symptoms.

A Phased Approach: The Elimination and Reintroduction Stages

The AIP diet is a two-phased protocol designed to identify individual food intolerances.

The Elimination Phase

This phase involves strictly avoiding known potential triggers for 30 to 90 days. The focus is on nutrient-dense foods like quality meats, organ meats, fish, most vegetables (excluding nightshades), fruits in moderation, healthy fats, fermented foods, and bone broth.

The Reintroduction Phase

Once symptoms improve, foods are slowly added back one at a time to monitor for adverse reactions. The goal is to create a personalized, sustainable diet.

AIP vs. Paleo Diet: A Comparison


Feature	Paleo Diet	Autoimmune Protocol (AIP) Diet
Primary Goal	General health, weight loss, and avoiding modern processed foods.	Targeted healing and reduction of autoimmune inflammation.
Key Inspiration	Ancient hunter-gatherer eating patterns.	The connection between diet, gut health, and autoimmunity.
Grains & Legumes	Generally avoided.	Strictly eliminated in the initial phase.
Dairy	Generally avoided.	Strictly eliminated, including ghee and butter, in the initial phase.
Eggs	Permitted.	Temporarily eliminated.
Nuts & Seeds	Permitted.	Temporarily eliminated.
Nightshades	Permitted (potatoes, tomatoes, peppers).	Temporarily eliminated.
Phased Approach	No formal phases.	Strict elimination and methodical reintroduction phases.

A Promising Tool in Autoimmune Management

Small-scale studies have shown promising results for AIP in managing conditions like inflammatory bowel disease (IBD) and Hashimoto's thyroiditis. For instance, a study in Inflammatory Bowel Diseases noted significant improvements in quality of life for IBD patients on AIP. AIP is considered a management tool alongside conventional treatments.

Conclusion

The origin of the autoimmune protocol diet stems from the Paleo movement and the work of Dr. Loren Cordain, refined into a systematic approach by Dr. Sarah Ballantyne. Focusing on the link between diet, gut permeability, and autoimmune inflammation, AIP offers a phased method to identify and address food triggers. Its evolution highlights growing interest in personalized nutritional strategies for chronic inflammatory conditions.

Frequently Asked Questions

While the AIP diet evolved from the Paleo diet concepts of Dr. Loren Cordain, it was systematized and popularized into its current form by Dr. Sarah Ballantyne, a medical biophysicist and author of The Paleo Approach.

The AIP diet is a more restrictive version of the Paleo diet, specifically targeting autoimmune disease. AIP eliminates a broader range of foods—including eggs, nuts, seeds, and nightshades—during its initial elimination phase and follows a structured reintroduction protocol.

The main theory is that by healing the gut lining and reducing intestinal permeability, or "leaky gut," the body's inflammatory immune response can be calmed, thereby reducing autoimmune symptoms.

The elimination phase involves removing all potentially inflammatory and immune-triggering foods for 30 to 90 days. It focuses on eating nutrient-dense, whole foods to support gut healing and reduce inflammation.

The reintroduction phase is crucial for identifying individual food triggers. By reintroducing eliminated foods slowly, you can determine which foods you tolerate and which exacerbate symptoms, creating a personalized, long-term dietary plan.

The duration of the AIP diet varies by individual. The elimination phase typically lasts for 30 to 90 days, or until symptoms improve significantly. The subsequent reintroduction and maintenance phases can continue indefinitely as a personalized dietary approach.

Yes, although research is still limited and primarily involves small, uncontrolled studies. Studies on IBD and Hashimoto's thyroiditis have shown that AIP may lead to significant improvements in patient-reported quality of life and symptoms.