Autoimmune disease, IBD, Hashimoto's
Autoimmune Protocol (AIP)
A strict paleo elimination aimed at calming autoimmune flares, then rebuilt through reintroduction.
- Core restriction
- Grains, legumes, dairy, eggs, nuts, seeds, nightshades, alcohol, additives
- Difficulty
- ●●●●●
- Check a food
- Open the food checker
A gentle reminder. This guide is for learning, not a prescription. Therapeutic diets interact with medication and conditions, so it's worth talking to your doctor or a registered dietitian before you begin.
A tidy few pages with the food lists, meal plan and reminders — good for the fridge door or the first appointment with your dietitian.
How it works
AIP starts from the hypothesis that certain foods increase intestinal permeability or provoke immune reactivity in people who already have autoimmune disease. It removes the suspected categories completely, then rebuilds the diet through structured reintroduction.
Evidence is early but not nothing: small trials in inflammatory bowel disease and Hashimoto's thyroiditis show meaningful symptom and quality-of-life improvements, though the studies were small, unblinded and included coaching support.
The elimination phase is 30-90 days. The reintroduction phase is the actual point, and the phase most people skip.
Nutrition at a glance
AIP is the strictest common elimination protocol, and it is explicitly designed to be temporary.
- Elimination phase
- 30-90 days
- Most people see any effect by week six
- Foods removed
- 8 groups
- Grains, legumes, dairy, eggs, nuts, seeds, nightshades, alcohol
- Reintroduction
- One food over 5-7 days
- Staged from least to most reactive
- Vegetables
- 8-9 servings/day
- The protocol is high in plants, not just low in foods
- Evidence base
- Small studies, IBD and thyroid
- Promising, not definitive
Nutrients that often run short
- Calcium
- Vitamin D
- Fibre
- Iodine
- Vitamin E
- B vitamins
These are the ones worth planning for — through food where you can, and through a supplement your clinician suggests where you can't.
Key cautions
None of this is meant to frighten you off. These are simply the things that most often catch people out on this diet — the ones worth raising at your next appointment.
- Talk to a clinician
Not a substitute for immunosuppressive therapy
In IBD, rheumatoid arthritis or lupus, stopping prescribed medication to trial AIP risks a flare that diet cannot rescue.
- Talk to a clinician
Skip it if you have a history of disordered eating
Removing eight food groups at once is a strong trigger for restriction, and the reintroduction phase is often the hardest part.
- Worth testing
Calcium and vitamin D need a plan
With dairy, nuts and seeds all out, most people need supplementation for the elimination phase.
- Keep an eye on
The reintroduction phase is the whole point
Staying in elimination indefinitely gives you no information and a narrow diet. Most people tolerate far more than they expect.
Used for
- Inflammatory bowel disease — Crohn's and ulcerative colitis
- Hashimoto's thyroiditis
- Rheumatoid arthritis and psoriatic arthritis
- Lupus and other connective tissue disease, as an adjunct
- Psoriasis and other autoimmune skin conditions
What to eat
Eat freely
Protein
- Grass-fed beef and lamb
- Poultry
- Wild fish and shellfish
- Organ meats
- Bone broth
Vegetables (non-nightshade)
- Leafy greens
- Broccoli and cauliflower
- Carrot
- Sweet potato
- Squash
- Beetroot
- Asparagus
- Onion and garlic
Fruit
- Berries
- Apple
- Citrus
- Banana
- Melon — two to three servings a day
Fats
- Olive oil
- Avocado and avocado oil
- Coconut oil and coconut milk
- Animal fats
Eat with care
Reintroduce in stages, one every 5-7 days
- Stage 1: egg yolks, ghee, seed-based spices, legumes with pods
- Stage 2: seeds, nuts, egg whites, cocoa
- Stage 3: dairy, white rice, gluten-free grains
- Stage 4: nightshades, alcohol, other grains
Best to skip
Grains and legumes
- All grains including rice and corn
- Beans
- Lentils
- Peanuts
- Soy
Animal and plant proteins
- Eggs
- All dairy
- Nuts and seeds
- Coffee (seed-derived)
Nightshades
- Tomato
- Potato
- Peppers and chilli
- Eggplant
- Paprika and cayenne
- Goji berry
Other
- Alcohol
- Refined sugar
- Seed oils
- NSAIDs where your doctor agrees
- Food additives and emulsifiers
Three days of meals
Day 1
- Breakfast
- Salmon patties with sauteed kale and half an avocado.
- Lunch
- Big salad with roast chicken, carrot, cucumber, olive oil and lemon.
- Dinner
- Beef and vegetable stew in bone broth with sweet potato and celery.
- Snack
- Apple slices and coconut butter.
Day 2
- Breakfast
- Leftover stew — AIP breakfasts do not need to be breakfast food.
- Lunch
- Tuna-free salmon salad with avocado mayo over greens.
- Dinner
- Roast chicken thighs, roasted squash, broccoli in olive oil.
- Snack
- Blueberries.
Day 3
- Breakfast
- Sweet potato hash with ground pork and spinach.
- Lunch
- Prawn and mango salad with coriander and lime.
- Dinner
- Lamb shoulder, cauliflower mash, roasted beetroot.
- Snack
- Cup of bone broth.
Getting started
- 1
Batch cook. AIP fails on logistics far more often than on willpower.
- 2
Set an end date for the elimination — 30 days minimum, 90 days maximum — before you start.
- 3
Track symptoms weekly with the same measure you would report to your specialist.
- 4
Keep taking prescribed immunosuppressants and thyroid medication. AIP is an adjunct, never a substitute.
- 5
Plan the reintroduction ladder in advance so you are not improvising at the end.
Common mistakes
- Never reintroducing, and ending up with a permanently narrow diet and unnecessary anxiety around food.
- Under-eating carbohydrate and calories, which is common and leaves people exhausted.
- Reintroducing three foods in a weekend and learning nothing.
- Using AIP during an acute severe flare instead of getting medical treatment.
- Assuming a food that failed once fails forever. Retest later.
FAQs
Is AIP proven?
Not in the way a drug is proven. Small studies in IBD and Hashimoto's show benefit, and the coaching component makes effects hard to isolate. It is reasonable to trial with support, not reasonable to treat as established therapy.
How long until I know?
Most responders notice change within three to six weeks. If 90 days changes nothing, stop and rebuild your diet.
Do I have to avoid nightshades forever?
No. Nightshades are the last reintroduction stage precisely because most people tolerate them fine.
Stacking with other diets
- AIP is already grain-free and dairy-free, so it subsumes gluten-free and low-lactose diets.
- AIP plus low FODMAP is extremely restrictive; use it only short term with a dietitian.
- AIP's coconut, sweet potato and berry emphasis conflicts with low oxalate and low histamine.