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What Is The Autoimmune Protocol (AIP) Diet?

Learn about the phases, benefits, and risks of the autoimmune protocol (AIP diet) for Hashimoto's disease.
What Is The Autoimmune Protocol (AIP) Diet?
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The Autoimmune Protocol (AIP) is a way of eating with a specific goal: to help minimize pain, inflammation, and other symptoms of autoimmune diseases. By reducing exposure to foods known to trigger an inflammatory reaction and helping to heal the gut, the AIP diet can reduce symptoms that don't respond to the treatment of the autoimmune disease itself.


Paloma Health has recommended the AIP diet as a recommended approach for hypothyroid patients with Hashimoto's disease who remain symptomatic after treatment. In this article, we look at the AIP diet, how to follow the AIP, the benefits and downsides of the AIP diet, and other important considerations.


What is autoimmune disease?


In an autoimmune disease, the body produces antibodies that cause dysfunction in targeted organs, glands, and tissues. Hashimoto's thyroiditis and Graves' disease are autoimmune thyroid diseases. Other commonly known autoimmune diseases include rheumatoid arthritis, multiple sclerosis, lupus, celiac disease, psoriasis, type 1 diabetes, and inflammatory bowel disease (IBD). Common symptoms of autoimmune diseases include fatigue, joint and muscle pain, gastrointestinal problems, and damage to the targeted areas of the body.


There are various causes and triggers of autoimmune disease, including heredity and genetics, viral and bacterial infections, environmental exposures, chronic stress, and chronic inflammation.


Specifically, it's also known that chronic inflammation in the gut can cause the intestinal lining to become permeable. When the gut becomes more permeable – a condition called "leaky gut" – toxins and inflammatory foods can more easily pass through the gut lining, triggering immune reactions and, in some cases, an autoimmune disease.


According to AIP Certified Coach Stephanie Ulrich, "Hashimoto's is a disorder of your immune system. When you think about your immune system, it's important to remember that 70 to 75% of your immune system is located in your gut. That's why with autoimmune disease, we want to focus on supporting gut health, which will, in turn, support your immune system."


What is the autoimmune protocol (AIP) diet?

The AIP diet is a two-phase elimination diet. During Phase One – "Elimination" – you eliminate foods and ingredients that are known to trigger inflammation, allergies, or autoimmune flares and reactions.

These trigger foods are replaced by foods that are nutrition-rich, anti-inflammatory, and healing to the gut.


During the second phase – "Reintroduction" – you gradually reintroduce those trigger foods while monitoring your symptoms. That way, you can determine which foods are your longer-term triggers and can continue to avoid them after you finish the AIP.

Phases of the AIP: elimination and reintroduction


What is the "elimination phase" of the AIP diet?


The AIP diet starts with the Elimination Phase. During this phase, you remove foods, additives, and other substances considered inflammatory and autoimmune triggers.


Some experts recommend that you start slowly and eliminate specific foods – or categories of foods – one at a time until you have eliminated all of the target foods.


What foods should you eliminate during the elimination phase of the AIP diet?


You should eliminate the following foods, drinks, and products:

  • Grains, including wheat, oats, rice, amaranth, barley, buckwheat, bulger, corn, millet, quinoa, rye, sorghum, and spelt, and products made from grains such as pasta, bread, cereals, crackers
  • Legumes
  • Beans, including soy, and soy products like tofu and tempeh
  • Nightshades vegetables like tomatoes, peppers, eggplant, and potatoes
  • Goji berries
  • Dairy – all forms, including butter and ghee
  • Butter
  • Eggs
  • Coffee
  • Chocolate
  • Alcohol
  • Nuts, including nut butters and peanut butter
  • Seeds
  • Seed-based spices, including allspice, anise, celery seed, cumin, fennel seed, sesame seeds, mustard, nutmeg, and poppy seeds
  • Fruit and berry-based spices: allspice, anise, caraway, cardamom, juniper, peppercorn, sumac
  • Sugar, including sugar substitutes like xylitol, mannitol, and stevia
  • Refined and processed foods
  • Refined oils and seed oils like canola oil, sesame oil, and sunflower oil
  • Food additives, dyes, and thickeners
  • Chlorella
  • Spirulina


AIP diet experts also recommend eliminating tobacco products and non-steroidal anti-inflammatory drugs (NSAIDs) like ibuprofen and naproxen.

What can you eat on the AIP diet?


You have many food choices on the AIP diet, including:

  • Meat, game, and poultry – ideally organic, pesticide-free, free-range, and grass-fed whenever possible
  • Fish
  • Vegetables – except for nightshade vegetables
  • Tubers, including sweet potatoes, yams, taro, and artichokes
  • Fruit – in small quantities
  • Coconut milk
  • Avocado oil, olive oil, and coconut oil 
  • Fermented foods without dairy, such as kombucha, kimchi, coconut kefir, coconut yogurt, sauerkraut, pickles, and pickled vegetables
  • Leafy herbs without seeds, such as mint, basil, oregano, chives, cilantro, dill, garlic, parsley, rosemary, sage, thyme, and turmeric
  • Green tea and herbal teas from leafy herbs (i.e., mint tea)
  • Bone broth
  • Vinegars


Which lifestyle changes are part of the Autoimmune Protocol?

Lifestyle changes are integral to the AIP diet. Stephanie Ulrich recommends that you incorporate three key lifestyle components: "Sleep, stress, and movement—all three play an important role in modulating the immune system and supporting your gut health and hormone regulation, which are all critical for Hashimoto's."


According to Ulrich, we should aim for seven to nine hours of quality sleep per night because "sleep is the time when our body's repairing itself and, with autoimmune disease, we want enough repair time and restorative time.


Stress management and working on resiliency are also essential. Says Ulrich, "Stress puts us in this chronic state of fight or flight and increases our inflammation, leading to things like leaky gut and autoimmune issues. Some ways to reduce stress include mind-body techniques, such as deep breathing, yoga, meditation, and finding community and social connection."


Finally, getting some physical activity daily is essential. Says Ulrich: "It can be really simple things like taking a walk around the block, or gardening, dancing, even cleaning the house. So many things can count as movement. Be careful not to overexert yourself, however. When you overexercise, you add stress to your body and divert blood flow away from your digestive system.


How long should you follow the Elimination Phase of the AIP diet?

How long should you follow the Elimination Phase of the AIP diet? Typically, the phase runs at least 30 days, but ideally, a full 90 days. The goal is to experience a significant reduction in your symptoms.


During the Paloma Speakers Series event on the AIP diet, functional nutritionist Risa Groux shared her recommendation: "I would say if you were diagnosed a long time ago, or you have multiple autoimmune diseases, I recommend that you go 90 days. I really would recommend 90 days for anybody who can tolerate it."


What is the "reintroduction phase" of the AIP diet?


After the Elimination Phase, and assuming that you have noticed improvements in your symptoms, you can move into the Reintroduction Phase. Typically, it's recommended that you reintroduce foods slowly, in small quantities, and one at a time. You can then gauge your symptoms and response and watch for any worsening symptoms or reactions.


Stephanie Ulrich recommends starting the Reintroduction Phase with foods that are less likely to be chronic triggers. During the Paloma Speakers Series event on the AIP diet, she shared the following chart, showing recommended stages for reintroducing various foods.


During the Reintroduction Phase, your objective is to broaden your diet and reintroduce a wider variety of foods while identifying those trigger foods you should continue to avoid.


Ulrich explains: "Start at first eating a very small amount of foods. And then you're going to wait a couple of hours. How do you feel? And then you're going to try a little bit more, and then how do you feel? It's a slow reassessment, and I always recommend that everyone keep a symptom and food journal because you want to keep track of what foods you're trying, how you react, and symptoms."


Suppose you tolerate a normal portion of food well without any reaction. In that case, it can be included in your diet going forward. It would be best if you continued avoiding foods that cause a reaction or symptoms. Because food intolerances can change, you should periodically try again to reintroduce a trigger food to help determine if you are still reactive to it.


Benefits of the AIP diet


The AIP has many potential benefits for your autoimmune disease and health. Specifically:

  • The AIP diet may reduce leaky gut and help restore gut balance
  • The AIP diet may help reduce autoimmunity
  • The AIP may reduce inflammation – and inflammation-related symptoms.
  • The AIP diet may help reduce antibodies. During the Paloma Speaker Series presentation on the AIP diet, Risa Groux recounted how she had antibody levels above 1400 when she was first diagnosed with Hashimoto's. According to Groux, after intensive studying and putting into practice a long list of nutritional changes, "I'm now about 10 points away from normal antibodies!"

Finally, there's the best possible benefit of all: you'll end up feeling much better!

One recent study of women with Hashimoto's following a 10-week AIP program reported a significant improvement in health-related quality of life, including physical function, emotional well-being, and vitality. While thyroid and antibody levels didn't change during the 10-week study period, inflammation and symptoms decreased considerably.

In her article here at Paloma Health, "My Experience Starting the Autoimmune Protocol Diet," patient advocate Juliana Sweeny reported on her AIP success. "After just a few months, my antibodies lowered significantly. After a few days on AIP, some of my symptoms disappeared, while others took months to fade. Everyone's experience is different! Don't give up on AIP or dietary changes because your symptoms don't go away overnight. It took four solid months for my worst symptoms to disappear, but I have continued to see progress..."


Will the AIP diet help you lose weight?


Many people ask if the AIP diet will help with weight loss. While the autoimmune protocol is not a weight loss-focused diet, when you eliminate inflammatory and trigger foods – and processed and junk foods – you will likely experience some weight loss, according to Risa Groux. "Weight loss is a side effect of wellness, and the AIP protocol focuses on wellness," says Groux.


Downsides of the AIP diet


The AIP diet is not recommended if you are pregnant, are significantly underweight, are experiencing malnutrition, or have a history of disordered eating. Before making any significant dietary change, it's a good idea to carefully review your health situation with your doctor.


Suppose you don't plan out your meals. In that case, you may find it challenging to get a nutritionally balanced diet – or enough dietary fiber – during the Elimination Phase of the AIP diet. You may want to work with a nutritional expert to help you implement the AIP diet, develop recommended meal plans, and ensure that you get enough nutrition. If you need help, Paloma Health's thyroid nutritionists offer virtual consultations to help you craft a plan to better support your Hashimoto's with food and nutrition.


Because the Elimination Phase of the AIP diet is quite restrictive, eating away from home can be a bit daunting. Your best bet is to focus on simply prepared whole foods, like plain grilled meats, poultry, and seafood, steamed vegetables, and salads with AIP-friendly dressings. (Make sure that whoever prepares the food holds the spices, butter, or other condiments.)


The AIP diet is challenging for people who don't cook. But, for those who are determined to follow the AIP diet, the website A Clean Plate offers an affordable eBook, "28 Days of No-Cook AIP." Paleo on the Go also has a broad selection of AIP-compliant prepared meals and foods available through their AIP Meal Delivery service.


Students away from home can also find it difficult to follow the AIP diet closely. Check out this Paloma article on resources to help students do the AIP diet in college.


Finally, one of the biggest complaints about the AIP diet is having to give up coffee and caffeine! To help, Paloma has an informative article recommending 5 caffeine-free, AIP-friendly alternatives to coffee.


The AIP diet can be complicated. But there are books, websites, and many resources to help, including Paloma Health's free mobile app (available on iOS and Android), which offers comprehensive resources to help make adopting the AIP diet and lifestyle easier. 


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How strictly to follow the AIP diet to see results

In the Paloma Speaker Series event on the AIP diet, Stephanie Ulrich explained that you can customize and personalize the AIP diet and still enjoy the benefits. Says Ulrich: "Figure out what can you handle, where you are in your life at that moment, and stick with it and see how you feel. If you feel like you're not making progress, you may start investing a little bit more and try the Paleo Diet. Then move to AIP. You can still benefit greatly by experimenting without going the whole way."


Risa Groux agreed: "You might respond fine just taking out gluten, dairy, soy, and sugar. Everybody is different. Do what works best for you, and then give it your all. If your 'all' is 80% of the protocol, then do that. If it's 100%, great! But do what works best for you."


A note from Paloma Health


The AIP diet goes hand in hand with comprehensive care for your Hashimoto's and hypothyroidism. Paloma makes monitoring your thyroid function easy with the Paloma Complete Thyroid Blood Test kit. This kit measures Thyroid Stimulating Hormone (TSH), Free Thyroxine (Free T4), Free Triiodothyronine (Free T3), and Thyroid Peroxidase Antibodies (TPO), the test that identifies Hashimoto's. Paloma Health's at-home thyroid test kit comes with everything you need for sample collection and analysis of TSH, free T3, free T4, and TPO antibodies, with the option to add on a reverse T3 and vitamin D test.

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Paloma Health has an affordable and convenient solution when you need a diagnosis, treatment, or adjustments to your hypothyroidism care. Schedule a virtual visit with one of Paloma's top thyroid doctors to ensure you get personalized quality care for your hypothyroidism.


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Mary Shomon

Patient Advocate

Mary Shomon is an internationally-recognized writer, award-winning patient advocate, health coach, and activist, and the New York Times bestselling author of 15 books on health and wellness, including the Thyroid Diet Revolution and Living Well With Hypothyroidism. On social media, Mary empowers and informs a community of more than a quarter million patients who have thyroid and hormonal health challenges.

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