Skip to content

What exactly is the Autoimmune Protocol (AIP) diet?

What exactly is the Autoimmune Protocol (AIP) diet?

What exactly is the Autoimmune Protocol (AIP) diet?

The AIP diet, autoimmune paleo diet or autoimmune protocol diet is often recommended to patients that are suffering from a reactive autoimmune condition.  More and more research shows how our gut health influences everything from our weight, to our mood, to our cognitive ability. It can be the reason for chronic health conditions, the root of our depression, and of course, the cause of our digestive issues. That’s why testing the health of our gut and then healing our gut with diet is essential for improving our mental and physical health.(1)

If you have an autoimmune condition, the Autoimmune Protocol (AIP) is an effective diet and lifestyle protocol that helps autoimmune patients overcome the core underlying factors preventing recovery, including inflammation, leaky gut, hormone imbalances, blood sugar imbalances, micronutrient deficiencies, and immune system dysregulation.(2)

A Functional Medicine approach will help you get to the root of your ill-health, design a tailored diet, reduce your symptoms and support you to feel truly well and full of energy every day.

What is an autoimmune condition?

A healthy immune system is designed to produce antibodies that attack foreign or harmful cells in your body. 

However, in people with autoimmune disorders such as rheumatoid arthritis, lupus, IBD, type 1 diabetes, Hashimoto’s, Graves disease and psoriasis, the immune system tends to produce antibodies that, rather than fight infections, attack healthy cells and tissues. 

Autoimmune diseases are thought to be caused by a variety of factors, including genetic propensity, infection, stress, inflammation and medication use. 

Also, some research suggests that, in susceptible individuals, damage to the gut barrier can lead to increased intestinal permeability, also known as “leaky gut”, which may trigger the development of certain autoimmune diseases.  We commonly find high zonulin levels in our autoimmune patients, a substance excreted by the tight gap junctions in the intestinal wall when they are under stress and more permeable.

Certain foods are believed to possibly increase the gut’s permeability, thereby increasing your likelihood of leaky gut. This in turn increases food intolerances and increases reactions and drives the autoimmune loop that many patients cant get out of prior to obtaining suitable clinic treatment.

What is the Autoimmune Protocol diet?

The Autoimmune Protocol (AIP) diet is purported to reduce inflammation, pain, and other symptoms experienced by people with autoimmune conditions by healing their leaky gut and removing potentially problematic ingredients from their diet.(3)

Many people who follow the AIP diet report improvements in the way they feel, as well as reductions in common symptoms of autoimmune disorders, such as fatigue and gut or joint pain. 

It’s important to acknowledge that an AIP diet is not a cure, and it may not be enough to put a disease into full remission or heal damaged tissues. Further support such as medication or targeted AIP supplements may be necessary to maintain the body’s optimal functioning. There is no shame in using conventional medicine in addition to a dietary and lifestyle approach to healing.(4)

Our approach at Advanced Functional Medicine is do assess the biochemistry of our patients, remove any healing blocks (such as parasites, intestinal permeability, food triggers, methylation and biochemical pathway disruptions) and rebalance the body allowing the body to heal and stop the autoimmune cycle progression.

How does the AIP work?

The AIP diet is an extension of the Paleolithic diet,(5) similar both in the types of foods allowed and avoided, as well as in the phases. Some people view the AIP as a stricter version of the paleo diet. 

The diet must be very basic and simple so as not to trigger inflammation in the intestines and further worsen leaky gut and autoimmune flare-ups.

The AIP focuses on:

Gut health: Gut inflammation, gut dysbiosis (imbalances in gut bacteria), and a leaky gut lining contribute to poor absorption of nutrients and systemic inflammation that feeds the autoimmune response. In the diet, foods that irritate the gut lining are avoided, while foods that support gut health are included.

Nutrient density: Every system in the body needs a wide array of nutrients to function at its best, including the immune system. Nutrient-dense foods are central to the diet, giving the body the tools it needs to heal deficiencies and support immune system function.


Blood sugar balance: High and low blood sugar can lead to systemic inflammation, immune flares, hormonal imbalances, and compromised brain function. Supporting balanced blood sugar is critical for recovery from any inflammatory condition. The autoimmune diet gives you the tools to support healthy blood sugar balance.


Immune system regulation
: Inflammation, leaky gut, hormone imbalances, blood sugar imbalances, and micronutrient deficiencies all contribute to immune system dysregulation. By reducing bacterial overgrowth and inflammation in the gut, removing food-borne immune triggers from your diet, providing dense nutrition and supporting blood sugar regulation, the autoimmune diet helps to support healthy immune function.(6)

The AIP diet consists of two main phases: you eliminate foods that are known to drive inflammation and resulting symptoms, and then you reintroduce foods methodically to rule out reactivity.

The elimination phase 

The elimination phase involves the removal of foods and medications believed to cause gut inflammation, imbalances between levels of good and bad bacteria in the gut, or an immune response. 

The length of the elimination phase of the diet varies, as it’s typically maintained until a person feels a noticeable reduction in symptoms. On average, most people maintain this phase for 30–90 days, but some may notice improvements as early as within the first three weeks.

Foods to avoid

  • Grains, beans and legumes: including products made from peanuts and soy, which are legumes. Grains and legumes are high in proteins called lectins. Lectins have been shown to degrade the intestinal barrier, adding to leaky gut. They can also be transported through the damaged intestinal wall into the bloodstream, where they may bind to insulin receptors and leptin receptors. Some believe lectins may also have the ability to desensitize these receptors, thus contributing to insulin resistance and leptin resistance.

When transported through the gut wall into the blood stream, lectins can also set off an immune reaction that further damages the intestinal wall and sets off systemic inflammation, further supporting the autoimmune reaction.

  • Gluten: Offering no real nutritive value, gluten wreaks havoc on the gut, leading to intestinal permeability (leaky gut) and eventually to autoimmune disease. But simply removing gluten and following a gluten-free diet, however strict, is not enough to ensure health and protection from disease. (7)  G  Gluten free alternatives should be removed also, this often contain many drains that will flare up patients and many of these foods are highly processed and cause reactions in patients. 
  • Nuts: Tree nuts are one of the top allergens and food sensitivities.
  • Seeds
  • Seed-based spices: These include anise, annatto, celery seed, coriander, cumin, fennel, fenugreek, mustard, nutmeg, poppy seed, sesame, allspice, star anise, caraway, cardamom, juniper, peppercorns, sumac and whole vanilla bean.
  • Dairy: this includes dairy from sheep or goats and raw dairy.
  • Eggs – often reactive in patients with autoimmunity, particularly egg whites we find
  • Corn: The protein in corn is similar enough to that in wheat and wheat-like grains that it can provoke an immune response.
  • Nightshades: Nightshade vegetables include eggplant, goji berries, sweet and hot peppers, hot pepper sauces, tomatillos, tomatoes, and white potatoes. Nightshades contain digestion-resistant and gut-irritating lectins, saponins, and capsaicin (a steroidal stimulant) that can contribute to leaky gut and pass through the gut lining, contributing to inflammation.
  • Nightshade-based spices: These include cayenne, chili powder, paprika, red pepper, and curry.
  • Refined and processed oils and vegetable oils
  • Sugars and sweeteners, including natural ones
  • Artificial sweeteners
  • Emulsifiers, thickeners, and other food additives: guar gum, carrageenan, xanthan gum, cellulose gum, soy lecithin, and other additives.
  • Alcohol
  • Hidden sources of gluten: Always read the labels as gluten is hidden in many foods and additives. Beware of non-specific ingredients such as “natural flavourings.”
  • NSAIDS: Non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen inflame the gut so avoid if possible.
  • Other: Avoid canned foods, processed foods, wheat grass, barley grass, brown rice protein, pea protein, hemp protein, liquorice root, aloe, slippery elm bark, commercial egg replacers, supplements containing ashwagandha (a nightshade) or oat seed, and immune stimulants such as chlorella and spirulina. (8)

Foods to eat

  • Most organic vegetables: include as much variety as possible, making sure to include the full colour spectrum.
  • Quality meats: If possible, select hormone-free, antibiotic-free, and pastured meats.
  • Organ meats and offal: Organ meats provide concentrated forms of nutrients.
  • Glycine-rich foods: Include foods containing connective tissue, organ meat, joints, skin, or bone broth.
  • Bone broth: It helps your immune system return to normal functioning through several different mechanisms, including building a healthy gut lining and providing many key minerals and amino acids. (9)
  • Fish and shellfish: Seek out ocean-caught cold water, low-mercury fish with high fat content. Swordfish, most tuna, and king mackerel are very high in mercury.
  • Quality fats: Choose pasture-raised, grass-fed animal fats, fatty cold-water fish, olive oil, avocado oil, coconut oil, and low-mercury Omega 3 supplements.
  • Low glycaemic organic fruits: Eat fruits lower in sugar and eat them with fat, fibre, or protein to slow the uptake of sugar.
  • Edible mushrooms: Mushrooms are generally fine for most individuals. However, some people with autoimmune conditions may react to immune-stimulating fungi such as Maitake and mushroom-derived beta-glucan, so monitor your response.
  • Probiotic and fermented foods: Fermented foods include sauerkraut, kimchi, fermented pickles (not packed in vinegar), coconut yogurt, kombucha, water kefir, and coconut milk kefir. You may need to make your own or buy one of the few brands that are genuinely fermented and free of sugars or additives.  These foods feed bacterias, good and bad some can cause a reaction in some patients prior to treatment that have gut dysbiosis.
     
  • Coconut: Enjoy coconut and coconut products that are free of sugars or additives, only in moderation, the focus should be quality protein and vegetables.
  • Herbs and spices: Avoid herbs and spices that are nightshades. Good options include basil, cilantro, cinnamon, coriander, clove, garlic, ginger, horseradish, lemongrass, mace, mint, oregano, parsley, rosemary, sage, saffron, sea salt, thyme, turmeric.
  • Vinegars: Avoid grain-based vinegars and instead choose apple cider, balsamic, champagne, coconut, red wine, sherry, ume plum, or white wine vinegars.

The reintroduction phase

Once you start to see a reduction of symptoms and improvement of overall well-being, the reintroduction phase can begin. During this phase, the avoided foods are gradually reintroduced into the diet, one at a time, , allowing for a period of 5–7 days before reintroducing a different food, based on the person’s tolerance. 

The goal of this phase is to identify which foods contribute to a person’s symptoms and reintroduce all foods that don’t cause any symptoms while continuing to avoid those that do. This allows for the widest dietary variety a person can tolerate. 

Foods that are well tolerated can be added back into the diet, while those that trigger symptoms should continue to be avoided. Symptoms vary and can include digestive upset, mood changes, fatigue, pain, sleep issues, brain fog, skin rash, or respiratory issues.

Keep in mind that your food tolerance may change over time so you may want to repeat the reintroduction test for foods that initially failed the test every once in a while. 

If you have a reaction to a food reintroduction, you must wait until those symptoms are completely gone before moving on to the next reintroduction, at least 4 days.

How long do I need to follow the AIP?

Sticking to the AIP diet for a minimum of 30 days gives your body a chance to begin calming the autoimmune response, healing the gut lining, reducing inflammation and repairing damaged tissues that were subject to the autoimmune attack. (10)

Many follow the AIP diet for 30 days to a few months before they start reintroducing foods, depending on the severity of the condition, 3 months provides a great window period for the body to heal with rebalancing the body. (11)

How we can help 

Achieving optimal nutrition is key to preventing and reversing autoimmunity and other chronic conditions. AIP isn’t necessarily easy – it definitely takes commitment, but if you have an autoimmune condition and you want to get on top of it, then you’re going to need to follow an AIP diet while treating other imbalances.

Combined with good sleep habits, managing stress levels and exercise, our Functional Medicine health practitioners can support you to figure out where your food sensitivities lay and what foods will help you to live well.  

We use Advanced Testing to fully assess our patients biochemistry, removing key blocks that may be preventing recovery, balancing important biochemical pathways such as methylation and repairing the gut.

Contact us now to find out more.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

Leave a Comment