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What is the Autoimmune Protocol (AIP)?

Joy Cutrone, Wellness & Certified AIP Coach, FMCHC-Candidate
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The Autoimmune Protocol Diet and Lifestyle Plan

The Autoimmune Protocol is a method of establishing the widest diversity of foods than an individual can eat by approaching it systematically. It includes an elimination and reintroduction phase of foods, as well as mindfulness around stress management and detoxification.

The dietary focus

For 30 to 90 days, you eat a baseline of a diverse set of foods that are free from most every antagonistic trigger. Don’t worry, it’s not a diet of deprivation – far from it, and there are a lot of great recipes, bloggers and coaches available to help – it’s a diet of planning and intentional food choices. Then, once your symptoms clear up, you add back foods you miss one at a time, not unlike a standard elimination diet but again, a bit more prescriptive and intentional based on years of earned experience and scientific study. If you experience no symptoms, then you can add in another food. And so on, until you achieve the widest diversity of foods that you can eat that support your health.

It’s an excellent system that is literally improving the lives of thousands of people suffering from autoimmunity as we speak.

Individualization: AIP to Your List

To really learn what an individual can tolerate and to take deeper action to calm inflammation, an Autoimmune Protocol diet is quickly emerging as the definitive dietary approach to try. In the absence of data about YOUR specific food triggers (or those of your loved one), contentious foods are automatically put on the AVOID list in the AIP diet TO START. So, in combination with the Paleo diet that forms its basis, this diet goes a step further to avoid:

  • all grains
  • all legumes
  • all dairy
  • Eggs
  • Nuts
  • Seeds (including cocoa, coffee and seed-based spices)
  • Nightshades (potatoes, tomatoes, eggplants, sweet and hot peppers and spices derived from peppers)
  • Potential Gluten cross-reactive foods.
  • Alcohol
  • NSAIDS (non-steroidal anti-inflammatory drugs, i.e. acetaminophen and ibuprofen)


  1. The elimination phase of the diet eliminates a BROAD set of foods based on a scientific understanding of what foods are potentially inflammatory. Once symptoms have subsided, you can begin to reintroduce foods so as not to be more restrictive than you need to be. Be sure to follow the protocol for reintroduction so that you observe the results and adapt accordingly, and to do so under the guidance of your trusted functional medicine practitioner, as reactions can be pronounced when reintroducing foods. A certified AIP coach can help you navigate the process.
  2. There are foods you CAN eat on this diet, even in the elimination phase. Paleo On the Go even has a dedicated menu for AIP dieters – and you may be shocked to see the list of delicious foods. It does cost to buy readymade, make no mistake about it – but that may be an acceptable price to pay to get something GOOD and DELICIOUS on board in the early stages of learning how to plan menus and/or combat a sense of deprivation that can set in when all this information is brought on board in the early stages of recovery.
    1. Autoimmune Families Community members get a $15 discount on orders from Paleo On the Go, so that can help take out the sting a bit, although the foods are fully prepared, and can be costly, depending upon your food budget.
    2. SunBasket is also a food delivery service of Paleo foods in the U.S., but with SunBasket, you do the cooking. So this enables you to eliminate some meal planning and get the ingredients home without shopping for them, while you make the meals in about 30 minutes. We use this to ensure we have compliant foods on the table on busy weeknights. Everyone in the family loves them – teenagers and all.
    3. The Real Plans meal planning service is another way to eliminate the burden of meal planning. This is a leg up that’s much more affordable than actually getting the foods in-house, as in options a & b. You need to do the shopping, but you just pick the meals you want and the shopping list is generated for you. This is a low-cost monthly subscription plan.
    4. Most affordable of all money-wise is to pull from among the many AIP recipes that can be found online, such as at The Paleo Mom AIP Recipes and at AIP Lifestyle, for example. Here you’re spending more time and less money. There is an ever-growing list of AIP bloggers, as well. See our Resources directory for more information.

Reintroducing foods

Mickey Trescott has a good article about reintroducing foods (1), and Eileen Laird has an an affordable, more comprehensive eBook you can buy for reintroducing foods on the Autoimmune Protocol.(2) Generally, you introduce a small amount of a new food, sometimes measured by the teaspoon, and observe symptoms for 2-3 days before introducing more. If you don’t have a reaction, then you would eat a lot of that food and watch for a reaction, if your practitioner agrees with this approach for that food for you. Note any symptoms. Then, if you do have a reaction, you would re-eliminate that food, and then get back to baseline before reintroducing another new food. In this protocol, you never reintroduce more than one food at a time, so that any symptoms are clearly attributable to that food.

If you choose to follow the Institute for Functional Medicine’s elimination dietary protocol (3) discussed above instead of the AIP elimination diet, then you’ll want to follow their plan for reintroducing foods. In this approach, you choose one food and eat that several times a day for several days to see what, if any, changes you observe in your body.

Another option for the IFM elimination diet approach is to use Dr. Amy Myers’ protocol for reintroduction. Dr. Myers is a noted functional medicine practitioner, protégé of Dr. Mark Hyman, and an expert on autoimmunity, especially thyroid-related disorders. She has a recommended protocol for adding back foods to your diet after completing a general functional medicine elimination diet. Take a look at Dr. Myers’ specific plan for doing that, which she provides as bonus material when you buy her book, The Autoimmune Solution (which we can’t provide here, since it’s gated content). Dr. Myers also offers a 6-week paid “Autoimmune Solution” program that provides guidance and additional insight into this approach.

Whether the AIP or the IFM elimination diet, using a trusted elimination diet that you discuss with your trusted functional medicine practitioner can be the shortest path to understanding what an individual’s tolerances are, and help eliminate months and years of thrashing about trying to treat symptoms with seemingly mysterious cause.

Experts and resources for the AIP

  • Sara Ballantyne, The Paleo Mom, on AIP
    • Sarah also collaborates with Mickey Trescott and Angie Alt, who are coaches in her network
    • Autoimmune Families founder Joy Cutrone received her AIP Certified Coach certification from the collaborative training expertise of Sarah, and coaches Mickey and Angie
  • Mickey Trescott and Angie Alt of Autoimmune Wellness
  • Eileen Laird of Phoenix Helix on AIP
    • A great library of resources from the AIP food pyramid to a grocery list to FAQ
  • Other AIP recommended resources by The Paleo Mom
  • Real Plans, which is a meal-planning service that includes AIP as well as other diet options. Again, meal planning can make or break success on the AIP diet, where we can all use a little help in making food choices and preparing meals that include ingredients that are different from what we do automatically.

As devil’s advocates among educated experts, there are some who question whether the AIP diet is necessary, i.e. Dr. Sara Gottfried (4), and Dr. Doni Wilson (5). Dr. Doni is a respected Naturopathic Doctor and Certified Nutritionist in New York well versed in the 5Rs protocol, and who has a lot of expertise to offer in the areas of sleep and overall wellness. Dr. Doni called up the importance of individualization and diversification in 2010, which are important principles that are actually included in the dietary plan, and which point to the need for continued education to that end among practitioners and participants.

See Also

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