We all know that good food is medicine and that cleaning up our diets is often a key component of improving health. But it’s not only about adding healthy foods. For people with an autoimmune disease, like rheumatoid arthritis, celiac disease, or multiple sclerosis, seemingly healthy foods can trigger an inflammatory cascade. Enter the autoimmune protocol, an elimination diet that can tease out which foods are problems for you (and which you can eat freely.)

The theory behind the diet

In autoimmune diseases, the body confuses healthy cells and foreign invaders, causing the immune system to attack and damage normal cells. The exact cause of these disorders is unclear, but one prevailing theory is that of the leaky gut.

A normal, healthy gut is somewhat permeable: It lets water and nutrients travel from the gut to the bloodstream but keeps harmful substances from passing through the same way. Some people, however, have too much permeability, so toxins and other substances can slip through and cause bodywide inflammation and an autoimmune response.

Certain foods are believed to increase the gut’s permeability. The AIP diet eliminates those foods (temporarily) to give the gut a chance to heal and tighten up the weak spots that allow the toxins through.

Autoimmune diseases that may respond to the AIP include adrenal fatigue, ankylosing spondylitis, celiac disease, Hashimoto’s disease, lupus, multiple sclerosis, polycystic ovarian syndrome, psoriatic arthritis, rheumatoid arthritis, narcolepsy, lyme disease, type 1 diabetes, fibromyalgia, psoriasis, Crohn’s disease, and Graves’ disease.

It’s done in two phases: elimination and reintroduction.


The first step is to eliminate foods and medications that cause gut inflammation and permeability for about 30 days. (That’s how long it takes for the gut to heal.) In that time, you’ll want to avoid a variety of potential problem foods.

  • Additives and preservatives in store-frozen or packaged foods
  • Alcohol: Beer, liquor, wine
  • Coffee
  • Dairy: Milk, eggs, yogurt, cheese, cream, butter, ice cream
  • Gluten: Bread, baked goods, crackers, cereals, pasta
  • Grains: Rice, rye, quinoa, corn, oats, wheat, barley
  • Legumes: Black beans, pinto beans, lima beans, peanuts, soy, cocoa, lentils
  • Nightshades: Bell peppers, eggplants, tomatoes, potatoes, cherries, red spices, goji berries, and tomatillos
  • Non-steroidal anti-inflammatory drugs (NSAIDs): ibuprofen, naproxen, diclofenac, and aspirin
  • Nuts and seeds: Almonds, chia, cashews, pecans, pistachios, walnuts
  • Select spices: Allspice, anise, pepper, poppy seeds, celery seed, cumin, caraway, mustard, nutmeg, and fennel seed
  • Sugars: molasses, brown sugar, regular sugar, and any foods containing sugar
  • Tobacco.

Some people eliminate all of these foods at once, while others prefer a more gradual approach and cut one food group at a time. Ultimately, the clock starts once all of the foods are out of your diet. It’s a good idea to keep a journal to track how you feel as your body heals.

What you can eat

During the elimination phase of the AIP, stock up on anti-inflammatory foods:

  • Fats: avocado oil, olive oil, coconut oil, beef tallow, chicken fat
  • Fermented foods: sauerkraut, kimchi, kombucha
  • Fruits: apples, bananas, berries, pears, peaches, mangos, and all other fruits, one to two servings per day
  • Flavoring: salt, cilantro, thyme, dill, cinnamon, basil, mint, rosemary, and most cooking herbs and spices, apple cider vinegar, coconut sugar, honey, coconut flour, maple syrup or blackstrap molasses
  • Proteins: beef, lamb, chicken, pork, fish, turkey
  • Vegetables: yams, broccoli, cauliflower, carrots, cabbage, lettuce, mushrooms, onion, kale, arugula, cucumber, and all other leafy greens and organic vegetables (excluding nightshades).
  • Herbal teas not derived from seeds.


After three weeks, choose one food to reintroduce. The most common triggers are gluten and dairy, so they’re a good place to start. Don’t start a reintroduction during times of stress, after a poor night’s sleep, or when sick, as all of those factors can affect your results.

Eat a small amount of the food and wait 15 minutes to see if you have a reaction. If you don’t have symptoms, eat a larger portion and monitor how you feel for two to three hours. If you still have no reaction, eat a normal-sized portion of the food. Monitor any reaction to that food for one to two weeks. If you experience symptoms, like joint pain or fatigue at any time, end the test and note that the food is an irritant. If not, you can add the food to your safe list. Then choose the next food item on the list to add. Test one food at a time until you’ve worked though the list.

Moving forward

The elimination phase of the AIP is short. You don’t have to live without everything on that list for the rest of your life, but you’re likely to find a few things you’d do best to avoid long-term. One study showed that the AIP reduces inflammation and encouraged remission in 78 percent of the study participants. Decreasing inflammation is a key factor in healing with an autoimmune disorder. Remember, 70 percent of your immune system is located in your gut.

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