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March 23, 2021 / Allison Koch, MS, RD, CSSD, LDN

Autoimmune Paleo Diet (AIP): The Comprehensive Guide

Wooden spoon, blue plate holding AIP Diet meal of grilled chicken, kale, cucumbers, apples, avocado, red onion, and parsley.

Autoimmune diseases affect over 24 million Americans, 80% of which are women and they are on the rise. What are they? A healthy immune system produces antibodies that attack foreign or harmful cells in your body. In a person with an autoimmune disease, the immune system produces antibodies that attack healthy cells or tissues rather than fight infections.

The exact cause is unknown, however, a variety of factors may contribute to their development including genetics, infections, chronic stress or inflammation, and certain medication use.

Symptoms vary depending on the condition – of which there are over 100 and can include fatigue, brain fog, joint pain, skin problems, digestive issues, recurring fever, or swollen glands.

Treatment focuses on reducing immune system activity and chronic inflammation – the latter of which may be managed through diet and lifestyle modifications like the autoimmune Paleo diet.

What is the Autoimmune Paleo Diet (AIP)?

Developed by Loren Cordain, PhD, founder of the Paleo diet, the autoimmune Paleo diet (also known as the autoimmune protocol diet) aims to help reduce inflammation, pain and other symptoms caused by autoimmune diseases by eliminating certain foods that may trigger inflammation.

If you know what the Paleo diet is, the autoimmune Paleo diet is similar, but is considered stricter. Like Paleo, the diet includes a number of food restrictions as well as two phases: elimination and reintroduction. In addition, the diet protocol emphasizes lifestyle modifications like prioritizing sleep, reducing stress, and regular physical activity as these can also influence symptoms.

While research is building on whether or not the diet works for treatment or symptom management, many people who follow it report less bloating, gas, arthritic joint pain, and a better quality of life. Let’s dive in deeper on what specific diseases the autoimmune Paleo diet might be helpful for.

What Types of Autoimmune Diseases Could the AIP Diet Help?

The autoimmune Paleo diet might be right for you if you have been diagnosed with an autoimmune disease and want to better manage your symptoms. By identifying the foods that trigger an inflammatory response, the diet helps reduce inflammation, promote gut healing and improve symptoms.

But it’s not for everyone. Groups that may not be suited to this diet include:

If you are considering starting the autoimmune Paleo diet, talk to your doctor and consider seeking a registered dietitian nutritionist (RDN) to help guide you through the process.

Leaky gut

Many individuals with autoimmune diseases have had chronic damage done to their gut barrier or lining, leading to increased intestinal permeability – also known as leaky gut. Normally the gut is lined with tight junctions that keep toxins and harmful bacteria out of the bloodstream while allowing nutrients to pass through so they can be transported to where they need to go in the body. With a leaky gut, those tight junctions have been weakened, allowing toxins to ‘leak’ into the bloodstream. The result is a chronic state of inflammation and malabsorption of nutrients that may contribute to development of autoimmune diseases. Symptoms of a leaky gut may include bloating, food sensitivities, fatigue, digestive issues, and skin problems.

Certain foods and lifestyle factors may increase the gut’s permeability, increasing the likelihood of leaky gut. The Paleo diet for autoimmune diseases focuses on eliminating these foods and replacing them with health-promoting, nutrient-rich foods that may help heal the gut while also reducing inflammation.

Skin conditions like psoriasis and eczema

Autoimmune diseases like psoriasis and eczema primarily impact the skin and results when the immune system is activated. The autoimmune Paleo diet may improve symptoms in people with psoriasis or eczema by helping to identify foods that contribute to inflammation, resulting in the skin condition, and avoiding them.

Inflammatory bowel disease

Inflammatory bowel disease (IBD) is when the immune system attacks the linings of the intestines, causing episodes of diarrhea, rectal bleeding, urgent bowel movements, abdominal pain, fever, and weight loss.

While long term and larger studies are limited, some research has suggested improvements in symptom management and quality of life when the autoimmune protocol diet is followed. In one small study, participants with IBD following the autoimmune protocol diet reported experiencing significantly fewer IBD-related symptoms by the end of the study despite no significant changes in markers of inflammation. Another small study reported significant improvements in IBD symptoms and quality of life after just three weeks of following the autoimmune Paleo diet.

Allergies such as hay fever

Seasonal allergies, like hay fever, are caused by an allergic response to outdoor or indoor allergens (like pollen, dust mites, and pet dander). Your immune system identifies the allergen as harmful and produces antibodies causing cold-like symptoms. The autoimmune Paleo diet may help with symptom management by decreasing the amount of inflammation associated with the allergic reaction.

Hashimoto’s thyroiditis

When a person has Hashimoto’s thyroiditis, antibodies produced by the immune system attack the thyroid gland, slowly destroying the cells that produce the thyroid hormone. One 10-week study in 16 women with the disease found decreases in inflammation markers and disease related symptoms by 29% and 68% respectively when following the autoimmune Paleo diet. Study participants also reported improvements in quality of life despite not seeing any significant differences in their measures of thyroid function.

Rheumatoid arthritis

The immune system produces antibodies that attack the linings of the joints in people with rheumatoid arthritis causing swelling and pain. A 2017 review study on dietary interventions for managing rheumatoid arthritis found that elimination diets, similar to the autoimmune Paleo diet, may help with symptom management by reducing inflammation.


People with lupus develop autoimmune antibodies that can attach to tissues throughout the body. The joints, lungs, blood cells, nerves, and kidneys are commonly affected. In addition to treatment, the autoimmune protocol diet may help reduce lupus inflammation and flares, but research is limited.

Celiac disease

Celiac disease results when the body has an immune reaction to eating gluten, a protein found in wheat, barley, and rye. Over time, the reaction creates inflammation that damages the lining of the small intestine and prevents absorption of certain nutrients. Treatment includes a strict gluten-free diet. The autoimmune Paleo diet restricts gluten as well as other foods that may contribute to inflammation. If followed immediately after diagnosis, the diet may help the gut to heal. However, during the reintroduction phase of the diet, it is important that a person with celiac disease continue to eliminate gluten-containing foods and will need to do so for the rest of their lives.

How Does the AIP Diet Work?

The Paleo diet for autoimmune diseases starts with an elimination phase that includes a number of food restrictions followed by a reintroduction phase. Foods that may provide an inflammatory response when eaten are eliminated and replaced with nutrient-rich foods to help ‘heal the gut.’ Once the body has had time to ‘reset,’ the restricted foods are gradually reintroduced one at a time to see if there is a response and if a continued restriction is necessary.

The diet also emphasizes lifestyle modifications like prioritizing sleep, reducing stress, and regular physical activity as these can also have an influence on symptoms of autoimmunity.

Due to the restrictive nature of the diet, it can be hard to follow and is not meant to be followed long term. Patients should notify their doctor or work with a registered dietitian nutritionist to ensure they are meeting their essential nutrient needs during both phases of the diet.

Elimination of certain foods from the diet

The first phase of the autoimmune Paleo diet is elimination and involves removal of foods believed to cause an inflammatory reaction, imbalances between good and bad bacteria in the gut, or that trigger an immune response. This includes grains, legumes, nuts, seeds, nightshade vegetables, eggs, and dairy. Tobacco, alcohol, coffee, vegetable oils, food additives, refined or processed sugars, artificial sweeteners and nonsteroidal anti-inflammatory drugs (NSAIDs) are also avoided.

What is allowed? Fresh, nutrient-rich foods that are minimally processed like some fruits, vegetables, certain meats and seafood, and non-dairy fermented foods. Stress management, better sleep, and increased physical activity are also emphasized.

The phase is followed until a person sees improvement in or reduction of symptoms–typically anywhere from 30 to 90 days.

Reintroduction of one food at a time

The second phase of the autoimmune Paleo diet is reintroduction and should not be started until an improvement in symptoms is seen. During this phase, the avoided foods are gradually reintroduced into the diet one at a time. The goal of this phase is to identify which foods may be causing a response and to continue to avoid those while adding back the foods that don’t cause a reaction.

Evaluation of reintroduced foods

When reintroducing a food back into the diet, follow this six-step process:

  1. Choose one food to reintroduce from the list of restricted foods.
  2. Eat a small amount of the food and wait 15 minutes to see if you have a reaction.
  3. If you don’t experience any symptoms, eat a slightly larger portion and monitor how you feel for the next few hours.
  4. If you don’t experience any symptoms, eat a normal portion of the food and then wait 5 to 7 days.
  5. After 5 to 7 days, if you haven’t experienced any symptoms, you can reincorporate the test food into your diet.
  6. Repeat this process with a new food from the restricted list.

If at any time during this process you experience symptoms or a reaction, end the test and continue to avoid the food. Reach out to your healthcare provider to let them know of the result so you can be properly tested for a food sensitivity, allergy, or intolerance.

Avoid reintroducing foods under circumstances that tend to increase inflammation and make it difficult to interpret results such as when you have an infection, after a bad night of sleep, high stress, or following a strenuous workout.

Types of Food to Eat on the AIP Diet

During the elimination phase of the autoimmune Paleo diet, consumption of fresh, nutrient-rich foods that are minimally processed are encouraged to help heal the gut. This includes:

Breakfast on the AIP diet

Breakfast might be the hardest to follow on the autoimmune Paleo diet as most of the typical breakfast foods are restricted. But it’s doable if you think outside the box. Sweet potato ‘toasts’ topped with a coconut-based yogurt, a drizzle of maple syrup, and a side of fruit. A veggie stir fry topped with sauteed ground turkey. Or leftovers from the night before. Here are some additional recipes from our database that would work:

Lunch on the AIP diet

For lunch, you’ll want to stick to lean meats, lots of veggies, and occasionally some fruit. Here’s a few recipes for consideration:

Dinner on the AIP diet

Dinner should include a nutrient-rich foods protein source like salmon, and a variety of vegetables like leafy greens and sweet potatoes. Here are a couple of ideas:

Snacks on the AIP diet

To keep energy levels up, you’ll want to be sure to include a couple snacks throughout the day that incorporate both protein and a carbohydrate-containing food. This can be a coconut based yogurt topped with fruit, a smoothie, or even leftovers. Here are some additional satisfying snack suggestions:

Foods to Avoid on the AIP Diet

The following foods are avoided during the elimination phase of the autoimmune Paleo diet to allow the gut time to heal while also reducing inflammation:

The Takeaway

The autoimmune Paleo diet meal planning, lifestyle modifications (stress reduction, sleep optimization etc.), and physical activity, may help improve symptom management, reduce inflammation, and ultimately improve quality of life in those that suffer from autoimmune diseases. As there is no known cure for autoimmune diseases, the autoimmune Paleo diet aims to help identify foods that may trigger symptoms so they can be avoided. It is not meant to be followed long term and due to the restrictive nature of the diet, it’s not for everyone. Work with your healthcare provider to determine if it’s right for you for helping manage your autoimmune disease.

Allison Koch, MS, RD, CSSD, LDN
Sports Dietitian, Nutrition Communications Professional, Running Coach

Allison Koch is a Chicago-based Registered Dietitian, Board Certified in Sports Dietetics, and a Road Runners Club of America Certified Running Coach. She has a private practice aimed at helping endurance athletes improve their nutrition to optimize their workouts and achieve peak performance. In addition to helping endurance athletes fuel up, Allison is a runner who uses her personal experience on the roads and trails and applies it to the clients she works with so that they can see results for themselves. She has completed 18 marathons since 2008 and is almost always training for her next endurance effort. You can follow her on Twitter, Facebook and Instagram

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