The Autoimmune Protocol (AIP) is a treatment strategy for autoimmune disease.

It can also be used help to ensure that a genetic predisposition to autoimmunity does not progress to a full-blown illness, and can be effective for treating other chronic health conditions.

Matthew and I have been on the AIP for over four years, with dramatic results.

The Origins of the AIP

Dr Loren Cordain published the first book about the 'paleo diet' in 2001 and co-wrote the paper Origins and evolution of the Western diet: health implications for the 21st century in 2005.

In 2007, Dr Terry Wahls began experimenting with a paleo diet in an attempt to manage her disabling Secondary Progressive Multiple Sclerosis (MS).

In 2011 she shared her results in a TEDX talk that spread rapidly, enabling ordinary people who were suffering from autoimmune disease to learn from her successful reversal of MS.

By that time, ancestral eating and lifestyle practices were being popularized by advocates like Mark Sisson. That was the year I began eating a paleo diet and experienced an alleviation of all my inflammation-related symptoms.

Early AIP

The AIP is a specialized version of the paleo diet, that includes specific lifestyle components.

When Matthew and I started the AIP in 2013, he was almost completely disabled by psoriatic arthritis and side-effects from the medications he had been taking to treat it for many years. A regular paleo diet had not helped him.

At that time, scraps of information about the AIP were available online. A handful of blogs. One e-cookbook had just come out: Mickey Trescott's Autoimmune Paleo (still a best seller).

Those of us who were experimenting with the AIP and blogging about it found each other online. We pieced together information about the protocol and shared what we found.

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Then The Paleo Approach by Dr Sarah Ballantyne came out in early 2014. It documented the science behind the AIP, and put the protocol in the spotlight.

Four years later, the AIP is (almost) becoming mainstream. In 2017 there are a bunch of books on the market, written by some of the early AIPers:

Dr Sarah Ballantyne describes the origins of the AIP in this podcast episode. She credits Dr Terry Wahls as one of the key influencers for its development.

Dr Wahls describes her own n=1 experimentation that predated the AIP in this podcast episode.

The Autoimmune Protocol

The AIP is an evidence-based protocol that includes two components:

  1. An elimination diet, in which all potentially inflammatory foods are removed from the diet and replaced by foods with maximum nutrient-density; and
  2. Lifestyle components to support healing including sleep, stress management, and appropriate activity.


There are two phases to the AIP, plus a third that it may be wise to consider:

  1. The elimination phase;
  2. The reintroduction phase; and
  3. A return to the elimination phase during a subsequent flare or period of high stress.

1. The Elimination Phase

The elimination phase removes all non-compliant foods and adds nutrient-dense foods specified by the protocol. It is also the time to assiduously attend to the lifestyle factors of the procotol.

  • SAD to AIP in SIX is a proven online program that runs several times per year and supports the transition to the AIP from a Standard American Diet (SAD) over six weeks.

The more compliance with all the elements of the AIP during the elimination phase, the shorter it will be.

How short?

One to three months is sufficient for most people, at which time careful reintroductions can begin.

The elimination phase begins at the onset of the full protocol. not from the beginning of dabbling or easing in.

How do you know when the elimination phase is complete?

The elimination phase ends when measurable improvements in autoimmune symptoms have occurred. For most people, that will be within 30-90 days.

For Matthew, it took about seven months.

Why so long?

Three reasons:

  1. We started before we really understood all the components of the AIP and how they work together to promote healing. We were slow to introduce organ meat, for example, and Matthew was reluctant to give up coffee at first.
  2. Matthew has had psoriasis all of his life. The longer a body has been in autoimmune response, and the more tissue and organ damage that has resulted, the longer it takes to heal.
  3. Autoimmunity wasn't the only problem. Matthew also suffered from severe, undiagnosed gastrointestinal issues that perpetuated the inflammation in his system. These required additional troubleshooting with his Functional Medicine Doctor.

What do you mean by 'measureable improvements'?

Measurable improvements are observable and describable improvements in symptoms.

Here's an example of some of the data Matthew collected during the first few years of his AIP:

  • Autoimmune Symptoms are represented by the blue line (this was an overall measure of severity of psoriasis + severity of pain and stiffness from psoriatic arthritis).
  • Nausea levels are depicted in orange.
  • Painkiller use is shown in grey (Matthew finds it useful to track painkiller use separately, as it relates to his ability to cope with pain, not just pain levels).
  • Brain fog is a common symptom of systemic inflammation and autoimmune disease and is tracked in yellow on this graph.

2. The Reintroduction Phase

Dr Sarah Ballantyne outlines the reintroduction process in this downloadable pdf.

3. A (Periodic) Return to the Elimination Phase

At the beginning of the AIP, most of us just grit our teeth and put up with restrictions until we can get back to regular life.

The problem is that 'regular life' is probably part of what contributed to our illness. There may be no going back.

The lifestyle elements of the AIP may need to be in your life forever if you want to be well. And there may be times when returning to the elimination phase of the diet is necessary.

  • AIP Reset is a cost-effective program, designed to support a 30-day return to the elimination phase. Run by long-term AIPers and certified health coaches Joanna Frankham and Emma King.

Most AIPers get to know themselves really well. They know when they can relax the restrictions and when they need to tighten up their protocol.

The AIP, with reintroductions, becomes a lifestyle of choice for many of us, and going back to how we lived before loses its attractiveness.

The Autoimmune Protocol

The Food

In The Paleo Approach, Dr Sarah Ballantyne summarizes the dietary elements of the AIP:

  • Eat meat, poultry, fish, and shellfish;
  • Eat vegetables and some fruit;
  • Use quality fats for cooking;
  • Source the best-quality ingredients you can; and
  • Eat as much variety as possible.

This part of the protocol can be divided into the foods to remove during the elimination phase and the foods to add.

Foods to remove

During the elimination phase, remove:

  • All Grains, including 'pseudo-grains' like buckwheat, chia, and quinoa;
  • All Legumes, including soy;
  • All Dairy;
  • Eggs;
  • All processed vegetable and seed oils;
  • All food additives, including emulsifiers;
  • Non-nutritive sweeteners including added sugars, sugar alcohols and stevia;
  • Nuts and seeds including nut and seed oils and seed-based spices;
  • Nightshade vegetables including potatoes, tomatoes peppers and nightshade-based spices;
  • Alcohol, Coffee and Cocoa.

Foods to add

Unlike some of the foods that are eliminated for a period of time on the AIP, the foods that are added can be kept in the diet forever. They are some of the most nutrient-dense foods on the planet, and the nutrients they contain are necessary for human health:

  • Vegetables. A lot of them (Terry Wahls recommends 9 cups a day). Excluding nightshades, with an emphasis on leafy greens.
  • Organ meats. Regularly. For their extreme nutrient density
  • Fish, seafood and sea vegetables.
  • Healthy fats including coconut oil and animal fats from pastured sources.
  • Fermented foods, like sauerkraut.

What can I eat?

Eileen Laird created this AIP Grocery List post.

Angie Alt has a reference post about tricky foods on the AIP.

The Lifestyle Elements

The lifestyle components of the AIP are designed to address the non-dietary factors that contribute to and perpetuate inflammation, gut dysbiosis and, therefore, autoimmune disease.

They include:

  1. Sleep;
  2. Stress Management;
  3. Appropriate Movement; and
  4. Connection.

They often require an individualized approach for the best outcomes.


When Dr Sarah Ballantyne joined Rory, Jo and I on the Healing Protocols podcast, she recommended sleep as the first thing to tackle when approaching the AIP.

Find more information about sleep here.

Stress Management

Managing stress may be one of the most challenging elements of the protocol. This is where I have to work hardest on a daily basis, and the area where I get significant return on my investment of time and energy.

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Find more information about stress management here.


Many of us are not moving enough. Some of us are moving too much. Or more specifically, in a way that is causing a stress response in our bodies, which is de-railing our efforts to heal.

Finding the appropriate level of movement is a key element of the AIP and one we each need to fine-tune for ourselves.


 In their book The Autoimmune Wellness Handbook, Mickey Trescott and Angie Alt include connection with people and connection with nature as a core element of the protocol.

  • Find more information about connecting with people here
  • Find more information about connecting with nature here.

Featured Resource

Real Plans

Nutrient-dense food is at the heart of the Autoimmune Protocol. Real Plans helps you figure the food part out, so you can devote your time and energy to other things.

Real Plans offers fully customizable paleo, primal and Autoimmune Protocol meal plans and shopping lists. 

Make it easy.

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