The Autoimmune Protocol Diet (AIP)

AIP - Autoimmune ProtocolThe Autoimmune Protocol diet (AIP) is in the same family as the Paleo diet.  If your goal is to feel better, you will want to learn more about this diet. The AIP targets healing the gut and reducing inflammation.  These are both major triggers of Hashimoto’s thyroiditis. The diet exists in 2 phases.  The first is more intense and requires the elimination of a greater number of foods.   The second phase is for long term maintenance and does allow for the reintroduction of some of the foods you had to excluded in the first phase.

The AIP diet is intended to be followed in a strict manor.  This is necessary in order to fully eliminate inflammation and remove all potential triggers for autoimmunity. Following the diet 95 percent of the time will not have the desired results. The idea of following this diet strictly may seem daunting but keep in mind your end goal.  The potential to achieve a state of thriving with a disease that conventional medicine believes incurable hopefully out-ways the difficulties you fear.   According to Sarah Ballantyne, PhD. (the brain behind it is not possible to “cure” autoimmune diseases, but through changes in diet and lifestyle, it is possible to go into remission from autoimmunity, sometimes permanently.[i]  Now that’s a goal to shoot for.


Phase 1

For 6 to 8 weeks it is necessary to be extremely strict about the food you consume. Food in restaurants and friends’ houses, no matter how sensitive they are to your dietary needs, will almost always include things that are not permitted. Cooking at home is the only way to go if you are devoted to healing your gut and sending your autoimmune disease into remission, according to AIP diet advocate and Clinical Nutritionist Jessica Flannigan.[ii]


Foods you must avoid in Phase 1 of the Autoimmune Protocol Diet

  •  Nuts and Seeds (including oils like walnut, sesame and flax, and including culinary and herbal seeds like chia, cardamom, mustard, cumin and fennel)
  • Beans/Legumes
  • Grains (includes rice, quinoa and corn)
  • Alternative Sweeteners (like xylitol and stevia)
  • Dried Fruits/over-consumption of fructose (no more than 10 to 20 grams per day)
  • Dairy Products
  • Eggs
  • All Processed Foods
  • Alcohol
  • Chocolate
  • Coffee
  • Nightshades (tomatoes, potatoes, eggplant, peppers, mustard seeds)
  • Vegetable Oils (olive and coconut oil are okay)
  • Vinegars (except raw apple cider)


Foods you can eat in Phase 1 of the AIP

  • Vegetables (excluding nightshades)
  • Fruit (limit to max 20 grams of fructose per day)
  • All Coconut Products (except coconut nectar and sugar)
  • Fats: Extra-virgin olive oil, coconut oil, avocados, lard (from wild or free-range animals)
  • Fermented Foods (kombucha, coconut yogurt/kefir, fermented vegetables, kimchee)
  • Bone Broths (from wild/organic/free-range animals)
  • Grass Fed Meats (avoid poultry unless exclusively range-fed)
  • Seafood (only from pristine sources)
  • Grass Fed/Wild Organ Meats
  • Non-Seed Herbal Teas
  • Green Tea
  • Sweeteners: 1 tsp a day of either maple syrup or honey
  • Fresh Non-Seed Herbs (basil, parsley, cilantro, etc…)


Phase 2 of AIP

There are not as many restrictions on the maintenance AIP diet, however certain foods can NEVER be reintroduced. These include:

  •  Grains
  • Soy
  • Dairy
  • Eggs
  • Vegetable Oils (except above mentioned exceptions)



After you have made it through Phase 1, you can reintroduce many foods, however some of them may still trigger an inflammatory or immune response. It is best to reintroduce foods one at a time, not more than 1 new food per week. Use a 72-hour re-challenge, as this will show if you have a reaction, that would indicate that it is a food that should be on your long term or permanent avoidance list. Common symptoms which indicate that the food is still a trigger include lethargy, brain fog, digestive distress (gas, bloating, diarrhea, constipation), achy joints, brain fog, insomnia, fatigue, skin outbreaks, or any other painful or uncomfortable symptom. It helps to keep a food reintroduction journal and to eat enough of the food to illicit a response, eating it a few times on the first day, and then again on the fourth. Avoid the food on days 2 and 3, in order to allow the immune system time to build up delayed antibodies. This is the best way to know for sure if your body is still triggered by a particular food.


AIP Quick Tips

Remember that foods you have a known allergy to should be avoided even if they are on the okay list for AIP. Also, some people believe that immature legume seeds like green beans and sweet snap peas are okay for the AIP diet. Follow your intuition and focus on organic, non-gmo foods. Avoid industrially-raised meat or fish. Find your local organic grocery, farmer’s market or CSA. Make friends with an ethical hunter. Find support on this site’s forum pages to connect with other folks committed to thriving with Hahimoto’s through diet and lifestyle. Work with a qualified professional – a Functional Doctor, Naturopath, Clinical Nutritionist, or Holistic M.D. – to customize a diet plan for your body and life.


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