How To Use the AIP Diet for Autoimmune Relief

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How To Use the AIP Diet for Autoimmune Relief

What You Need to Know About the Autoimmune Paleo Diet

If you’ve been diagnosed with an autoimmune disease like Hashimoto’s thyroiditis or inflammatory bowel syndrome or have common symptoms of autoimmune conditions, like joint pain, brain fog, fatigue, or gut pain, you’ll be relieved to know that there are diet options that may help reduce your symptoms and improve your quality of life.

The Autoimmune Protocol, popularized by people like Sarah Ballantyne, Ph.D., and Mickey Trescott, NTP, has helped many people turn the tables on their autoimmunity, allowing them to live normal, productive lives. Let’s explore what autoimmune diseases are, what the autoimmune paleo diet is, how it helps autoimmune conditions, and how to use an autoimmune diet.

AIP diet: Cupcake with AIP sign

What Are Autoimmune Diseases?

Autoimmune diseases are when your body’s immune system mistakenly attacks your own tissues. Depending on which part of your body is being attacked, you may experience a wide range of symptoms, from fatigue to skin rashes, bloating, and chronic pain.

Autoimmune disorders affect approximately 16% of Americans and appear to be increasing in prevalence [1]. It’s also worth noting that a shocking 78% of autoimmune disease patients are women [2]. Most importantly, quality of life can be quite low for autoimmune patients whose disease is not under control.

Some of the most common autoimmune diseases are:

  • Inflammatory bowel diseases, like Crohn’s disease and celiac disease
  • Hashimoto’s thyroiditis and Grave’s disease
  • Rheumatoid arthritis
  • Lupus (Systemic Lupus Erythematosus or SLE)
  • Psoriasis
  • Multiple sclerosis (MS)
  • Type 1 diabetes

Symptoms of autoimmune diseases are highly variable, which can make autoimmune conditions difficult to diagnose. The most common symptoms of autoimmunity include:

  • Fatigue
  • Joint pain and swelling
  • Recurrent skin problems
  • Abdominal pain or digestive symptoms
  • Recurring fever
  • Swollen glands or lymph nodes

These symptoms are signs that your immune system is attacking your own body, and that your health needs attention. One way to provide that attention is through diet.

What Is the Autoimmune Protocol Diet?

Many autoimmune diseases are difficult to treat or to get under control. The good news is that the Autoimmune Paleo diet — also known as the AIP diet or the Autoimmune Protocolhas been shown to reduce autoimmune symptoms, and in some anecdotal stories has brought about full remission.

The autoimmune diet is an anti-inflammatory diet to remove potentially inflammatory foods that may aggravate your symptoms of autoimmune disease for a few weeks and then maintain your symptom relief by avoiding your worst triggers [3].

You do NOT have to follow the AIP diet just because you have an autoimmune condition. This is a mistake often made by autoimmune patients. The name should not be understood to mean it’s best for any AI condition. Rather, it’s just a starting point to help determine what foods feel best to you. 

As with any elimination diet, the primary purpose of the diet is not to do a strict diet forever but to help you identify your worst symptom triggers. That way, you can improve your quality of life, and make better progress with your other treatment. If you feel good on foods the diet says to avoid, that is OK and you should consume those foods.

Foods To Eat on the AIP Diet

AIP diet: a variety of green vegetables and fruits

Let’s explore what to eat on the AIP. While the AIP diet may remove a lot of foods, there are still a lot of delicious ingredients from which to make a satisfying meal.

The Autoimmune Paleo Diet is based on the Paleo approach. This diet focuses on eating nutrient-dense foods our Paleolithic ancestors would have eaten. These include:

  • Nose-to-tail grass-fed or wild-caught meat, fish, and fowl, including organ meats and bone broth
  • Healthy fats and oils such as coconut oil, olive oil, avocados and avocado oil, and coconut milk
  • A diverse array of fresh fruits and veggies, including sweet potatoes, greens, lettuce, cucumbers, zucchini, berries, apples, and melon
  • Fermented foods, including sauerkraut, kombucha, and kimchi
  • Herbs and spices not derived from seeds, such as cinnamon, turmeric, thyme, oregano, basil, and rosemary
  • Sweeteners such as stevia or maple syrup

Foods To Avoid on the AIP Diet

The Paleo diet avoids the most common inflammatory foods, like grains and dairy products.

The AIP diet removes a few additional food groups during the elimination phase because they seem to frequently trigger inflammation for people with autoimmune disorders. These foods include:

  • All grains
  • Eggs
  • All dairy products, including ghee, kefir, milk, cheese, and cream
  • All legumes, such as green beans, black beans, white beans, kidney beans, and garbanzo beans
  • Nightshade vegetables, including tomatoes, potatoes, peppers, eggplant, tomatillos, and spices derived from nightshades, like paprika, and cayenne pepper
  • All nuts and seeds, such as almonds, walnuts, and chia seeds, including their derivatives, like seed oils and vegetable oils (for example, canola oil, walnut oil, or almond flour)
  • Spices derived from seeds, including fennel, cumin, dill, anise, mustard, coriander, and nutmeg
  • Alcohol and coffee
  • Added or artificial sweeteners and food additives

You can see that the list of foods to avoid on the AIP is highly specialized and quite restrictive. For this reason, I only recommend you try a diet like AIP only after you have seen no improvement from a less-restrictive diet, like a standard Paleo diet. Do consider getting support from a health coach or dietician to create your personalized AIP Diet.

How To Do the AIP Diet:

There are three parts to any elimination diet: the elimination phase, the reintroduction phase, and the maintenance phase. Here’s how to work the AIP diet into your daily life for the best results.

Elimination Phase

To begin your AIP diet, eliminate eggs, grains, legumes, nuts and seeds, added sweeteners, alcohol,  nightshadeveggies, and processed foods. (If you’re already on the Paleo diet, you will have already given up a lot of these foods.)

If you’ve not seen any symptom improvement after 2-3 weeks, it’s likely that your symptoms are not related to foods you eliminated on the AIP diet.

If you do notice improvement, continue the elimination phase until your symptoms plateau.


Once your symptoms have plateaued, it’s time to begin reintroductions. Reintroduce one food at a time, and watch for symptoms. It’s most practical to start your reintroductions with the foods you miss most. Use a food diary to help you.

If you have a symptom flare after reintroducing a food, that food may need to stay out of your diet for a while longer. If you don’t notice any symptoms, you can safely include that food in your diet again.

Maintenance Phase

Once you’ve reintroduced all the foods you want to test, use what you learned to create a custom diet plan that minimizes your symptoms while you focus on improving your gut health and other treatments.

Tips for Using the Autoimmune Protocol

Woman looking upward with a checklist above her head

Making any diet change can feel overwhelming and challenging, so make it easy on yourself. Here are a few tips to help:

Keep it simple to start. Find a few basic recipes that sound good and use them to develop a simple meal plan. Once you’re comfortable with your dietary changes and know which foods trigger your symptoms, then research new recipes to expand your menu options.

Be prepared. Stock your pantry with ingredients you need for your basic meal plan, and remove all off-AIP plan foods. Make a few big batches of your simple starter recipes and load up your freezer.

Be as strict as possible about the diet for 2-3 weeks. This will help you feel better faster and give you better results during your food reintroductions.

Don’t stay on any diet too long if it’s not working. If you don’t notice any positive changes after a few weeks, consider trying something different.

Does the AIP Diet Work?

There is not yet much data specifically on the AIP diet, but the limited research we have is supportive and suggests that the AIP diet can improve the quality of life and symptoms for people with autoimmune conditions. Consider these study results:

  • An 11-week AIP diet for patients with active inflammatory bowel disease (IBD) improved their quality of life [4].
  • Women with Hashimoto’s thyroiditis improved their quality of life and symptoms by using the AIP diet for 10 weeks [5]. Their tests showed no significant changes to any measures of thyroid function or antibodies, but their inflammation decreased by 29%.
  • Inflammatory bowel disease patients who used the autoimmune protocol diet saw significantly improved IBD scores. Follow-up endoscopies after 11 weeks on the diet showed signs of mucosal healing in some patients [6].

The team that published these findings regarding mucosal healing later performed follow-up research to see whether there were measurable changes in inflammation in the large intestine after following the AIP diet. They found significant improvements in the patients’ endoscopy scores, indicating that the diet had reduced disease activity [7]. However, the study had a very small sample size, so larger trials will need to be completed to confirm these results.

A few additional studies of diet interventions that are similar to the AIP diet have found a reduction in symptoms, inflammation, or specific blood markers. The AIP diet is a nutrient-dense diet rich in omega-3 and omega-6 fatty acids, vitamins, minerals, and plant foods.

A 2020 systematic review found that a low-calorie, low-protein diet high in fiber, omega-3 and omega-6 polyunsaturated fatty acids, vitamins A, B, C, D, and E, as well as calcium, zinc, selenium, iron, copper, and polyphenols, improved symptoms and quality of life for lupus patients [8]. The AIP diet has a similar but not identical nutritional profile, but this result implies that diet can have an impact on autoimmune symptoms.

A second systematic review found that lupus patients treated with omega-3 fatty acids, vitamin D, turmeric, and a diet low in high-glycemic foods reduced inflammation and improved blood pressure and fatigue [9].

Finally, a 2019 systematic review found that various dietary patterns impact high-sensitivity C-reactive protein, a biomarker of inflammation) [10]. Three months of the Paleolithic diet reduced CRP from baseline marginally.

To date, no studies have shown that the AIP diet reduces antibodies, but symptom improvement is certainly its own just reward. There is enough inferential evidence here to warrant trying the AIP diet to see how your autoimmune condition responds, especially if you haven’t seen any symptom relief from a less-restrictive diet like the Paleo diet.

How Does the AIP Diet Work?

The development of autoimmune diseases is believed to happen at the intersection between your genetic predisposition [11], your gut health [12, 13], and current environment [14, 15, 16]. Intestinal permeability [17] (leaky gut) is thought to be particularly closely related to the development of autoimmune disease [18, 19, 20, 21, 22, 23, 24]. However, it hasn’t yet been clearly proven to be a direct cause of autoimmunity.

What we do know is that an out-of-balance gut bacteria can increase intestinal permeability [25, 26, 27], which can cause a cascade of inflammation and an overzealous immune response. We also know that inflammatory foods such as gluten [28], alcohol [29], or other food sensitivities can increase intestinal permeability and affect the makeup of the gut microbiome.

The Autoimmune Paleo Diet temporarily eliminates foods that are known to influence intestinal permeability, like gluten, alcohol, and sugar. It also begins by excluding foods that may trigger an immune response in some people, like dairy, eggs, nuts, seeds, and nightshadeveggies.

When you remove these triggers, inflammation decreases, and your symptoms may subside. This may help to heal your gut lining and calm your overactive immune response.

Probiotics have been shown to improve intestinal permeability [30, 31, 32], promote a healthy immune response in your gut [33, 34, 35], and balance the gut microbiome [36, 37]. This makes probiotics natural helpers for autoimmune patients. For more on how to use probiotics, see our Probiotics Starter Guide.

The Bottom Line

If you have an autoimmune disease and haven’t seen any symptom relief from a basic elimination diet like the Paleo diet, the Autoimmune Paleo Diet is a worthwhile option. It has been shown to reduce symptoms and improve quality of life for inflammatory bowel disease and Hashimoto’s thyroiditis patients, and similar dietary interventions have reduced inflammatory markers in autoimmune patients.

Confidently try the AIP diet by keeping things simple, creating a simplified meal plan, and preparing your pantry. Only stick with the diet after the first several weeks if you are seeing symptom improvement.

➕ References
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