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Yes, Where Do I Start?

A Guide to the AIP Diet For Beginners

When and How to Use the Autoimmune Protocol Diet for Hashimoto’s, IBD, and More

Key Takeaways:
  • The autoimmune protocol diet — also called the autoimmune Paleo diet — eliminates a wide variety of foods linked with triggering inflammation for those with autoimmunity.
  • The restrictive nature of the AIP diet means it shouldn’t be your first choice in dealing with autoimmune symptoms.
  • It makes sense to try a standard Paleo or reduced-carb (low FODMAP) regimen first, only moving onto AIP if these don’t produce good enough symptom improvement.
  • As well as gluten, AIP eliminates dairy, legumes, grains, nightshade vegetables (e.g. tomatoes, peppers, and potatoes), nuts, seeds, eggs, and seed-derived spices.
  • Some studies have shown the AIP diet can improve the symptoms of Hashimoto’s thyroiditis, IBD, and other autoimmune conditions.
  • After the initial elimination phase of the AIP diet, it’s important to reintroduce foods one by one, watching out for symptoms.
  • Over time you can use what you’ve learned about your food sensitivities to create a maintenance diet that works for you.

Being diagnosed with an autoimmune disease like Hashimoto’s thyroiditis or inflammatory bowel disease, or experiencing autoimmune symptoms such as joint pain, brain fog, fatigue, and gut pain can be distressing. But it’s good to know that various types of elimination diets, including the autoimmune protocol (AIP) diet for more intractable cases, may reduce your symptoms and improve your quality of life.

However, It’s important to understand that, in spite of the name, an autoimmune protocol diet is not necessary for everyone who has an autoimmune disease. You’d be better off trying less restrictive diets first and only moving onto the AIP if these don’t work for you (or this diet has been specifically recommended for you). 

The AIP diet can be a little daunting, but over time you’ll generally find a version of it that works for you. Once you know the basics of an AIP diet for beginners (which we’ll go through in this article), the rest is generally personalizing the diet to achieve the best results for your specific symptoms. Before getting into the details, here’s a quick overview.

How Diet Can Help Autoimmune Conditions

Autoimmune conditions include:

  • Hashimoto’s thyroiditis
  • Lupus
  • Rheumatoid arthritis
  • Multiple sclerosis
  • Graves’ disease
  • Addison’s disease
  • Celiac disease

Excessive inflammation underlies many autoimmune conditions [1], which is where changes to your diet can help. By removing potentially inflammatory foods that may aggravate your symptoms, you can achieve some symptom relief. Identifying your worst trigger foods and then continuing to avoid them can help to maintain your autoimmune symptoms at a lower level [2].

Here are some general principles for an elimination and reintroduction approach: 

  • Start with the least restrictive diet framework possible.
  • Follow your new diet for two to three weeks and observe symptoms.
  • If symptoms improve, gradually reintroduce healthy foods while monitoring how you feel.
  • If symptoms don’t resolve, try a more specialized diet. 

In my clinical experience, it’s usually best to start with a lighter intervention first. For many people with autoimmune illnesses, a Paleo diet, which focuses on unprocessed whole foods close to the pattern humans were eating in Paleolithic times, is sufficiently anti-inflammatory to ease symptoms. For others, the low FODMAP diet, which removes the fermentable carbohydrates that trigger some gut bacteria to produce a lot of gas, is helpful.

However, if neither of these diets works well, or if you experience just limited success with a standard Paleo diet, the more advanced AIP may be the best diet for you, at least in the short term.

Getting Started With AIP

There are three parts to any elimination diet: the elimination phase, the reintroduction phase, and the maintenance phase. Here’s how to work the AIP diet into your daily life for the best results.

AIP Diet For Beginners

Elimination Phase

You’ll likely already be gluten-free and dairy-free if you are eating Paleo. If this or a carb reduction (low FODMAP) diet hasn’t worked to resolve your autoimmune symptoms, the initial elimination phase of the AIP diet is more likely to have a symptom-easing effect because it cuts out a much wider range of foods, including eggs, grains, legumes, nuts and seeds, added sweeteners, alcohol, nightshade veggies, and processed foods. To get started on the elimination phase of AIP, check the guide below for a list of foods to eat or avoid).

AIP Diet for Beginners: A Food List

Fine to EatAvoid at First
Nose-to-tail grass-fed or wild-caught animal proteins, including meat, fish, fowl, organ meats, and bone brothAll grains, eggs, and legumes, such as green beans, black beans, white beans, kidney beans, and garbanzo beans
Healthy fats and oils such as coconut oil, olive oil, avocados and avocado oil, and coconut milkAll nuts and seeds, such as almonds, walnuts, and chia seeds, including their derivatives like seed oils and vegetable oils; for example, canola oil, walnut oil, and almond flour
A wide variety of fresh fruits and veggies, including sweet potatoes, greens, lettuce, cucumbers, zucchini, berries, apples, and melonNightshade vegetables, including tomatoes, potatoes, peppers, eggplant, tomatillos, and spices derived from nightshades, like paprika and cayenne pepper
Non-dairy fermented foods, including sauerkraut, kombucha, and kimchiAll dairy products, including ghee, kefir, milk, cheese, and cream
Herbs and spices not derived from seeds, such as cinnamon, turmeric, thyme, oregano, basil, and rosemarySpices derived from seeds, including fennel, cumin, dill, anise, mustard, coriander, and nutmeg
Stevia and maple syrupMost added or artificial sweeteners and food additives, plus alcohol and coffee

If you don’t see any symptom improvement after two to three weeks, it’s likely that your symptoms aren’t related to the foods you eliminated on the AIP diet.

If you do notice improvement, continue the elimination phase until your symptomatic improvements plateau.


Once you have reached a plateau, it’s time to begin reintroductions. Reintroduce one food at a time, and watch for any change in symptoms. It’s most practical to start your reintroductions with the foods you miss most. Use a food diary to help you.

If you have a symptom flare after reintroducing a food, that food may need to stay out of your diet for a while longer. If you don’t notice any symptoms, you can safely include it in your diet again.

If you do notice a symptom flare when reintroducing a particular food, try not to get discouraged! This doesn’t necessarily mean you’ll need to avoid the food forever. Your body may just need a bit more time to heal. Try reintroducing the food again after a few more weeks, or whenever you feel most comfortable.

Maintenance Phase

Once you’ve reintroduced all the foods you want to test, use what you learned to create a custom diet plan that minimizes your symptoms while you focus on improving your gut health and other treatments.

Tips for Success

Making any diet change can feel overwhelming and challenging at first, so to make the AIP diet for beginners easier, try these few tips:

  • Find a few basic recipes that sound good and use them to develop a simple meal plan. Once you’re comfortable with your dietary changes and know which foods trigger your symptoms, research new recipes to expand your menu options.
  • Stock your pantry with ingredients you need for your basic meal plan, and remove all off-AIP plan foods. Make a few big batches of your simple starter recipes and load up your freezer.
  • Be as strict as possible about the diet during the first two to three weeks. This will help you feel better faster and give you better results during your food reintroductions.

Research on AIP and Autoimmunity

Overall, studies of the AIP diet for autoimmune disease are still in short supply. But what we have adds credence to the hypothesis that it seems to help some people with autoimmune conditions. 

Consider these study results:

  • An 11-week AIP diet for patients with active inflammatory bowel disease (IBD) improved their quality of life [3].
  • Women with Hashimoto’s thyroiditis improved their quality of life and symptoms by using the AIP diet for 10 weeks [4]. After following the AIP diet for Hashimoto’s, inflammation in these women decreased by an impressive 29%.
  • Inflammatory bowel disease patients who used the autoimmune protocol diet saw significantly improved IBD scores. Follow-up endoscopies after 11 weeks on the diet showed signs of mucosal healing in some patients [2].

AIP and Autoantibodies

Autoantibodies (misguided, or pathogenic, antibodies produced in response to your body’s own proteins), are the hallmark of many autoimmune ailments. Higher levels of autoantibodies tend to correlate with a more significant autoimmune disease and greater clinical symptoms [5] When levels of these fall, it tends to imply improvement in a patient’s autoimmune condition. 

To date, no studies have shown that the AIP diet, specifically, reduces autoantibodies. However, a small-scale systematic review (6 case studies and 2 clinical trials) found the standard Paleo diet reduced thyroid antibodies and normalized thyroid hormones in Hashimoto’s thyroiditis and Graves’ disease [6].

More research is needed, but this is an encouraging finding. It implies that an anti-inflammatory diet in general, and potentially the AIP diet more specifically, may target the underlying causes of autoimmunity.

Other Nutrient-Rich Diets and Autoimmunity

A few additional studies of interventions similar to the AIP diet have also found encouraging improvements for people with autoimmune illnesses.

For example, the Wahls Paleo diet, which is similar to the AIP diet (i.e. a Paleo diet modified to reduce autoimmunity), improved fatigue, disability, and quality of life in those with relapsing-remitting multiple sclerosis according to one meta-analysis [7]. MS patients following the Wahls diet also experienced better mental health with reduced depression and anxiety [8]. 

In a nutshell, there’s enough inferential evidence to warrant trying the AIP diet for autoimmune conditions if you haven’t seen any symptom relief from a less-restrictive diet like the Paleo diet.

Downside of an AIP Diet

AIP Diet For Beginners

While the AIP diet can offer immediate relief for more complicated autoimmune cases, I am concerned the initial elimination stage can potentially result in nutrient deficiencies if you carry it on too long. Ultimately this may worsen the underlying issues that created the autoimmunity in the first place.

This is why I always recommend that you try a more moderate version of a paleo diet first. If you do progress to the AIP diet, it’s vital you move on to the reintroduction and maintenance phases as soon as you are able.

It might be worth having some professional help with these later stages of the AIP diet — you can reach out to us at the Ruscio Institute if you think this would benefit you.

Understanding Autoimmune Disease

Autoimmune disease happens because your immune system mistakenly attacks your own tissues. Depending on which part of your body is being attacked, you may experience a wide range of symptoms, from fatigue to skin rashes, bloating and other gut problems, thyroid health issues, and chronic pain.

Autoimmune disorders affect approximately 16% of Americans and appear to be increasing in prevalence [9]. Women account for 78% of autoimmune disease patients [10]. Quality of life can be low for autoimmune patients whose disease isn’t under control.

Some of the most common autoimmune diseases are:

  • Inflammatory bowel diseases, like Crohn’s disease and celiac disease
  • The thyroid disorders Hashimoto’s thyroiditis and Graves’ disease
  • Rheumatoid arthritis
  • Lupus (systemic lupus erythematosus or SLE)
  • Psoriasis
  • Multiple sclerosis (MS)
  • Type 1 diabetes
  • Swollen glands or lymph nodes

The Gut-Autoimmune Link

Your genes and stress level are two factors that can affect your chances of developing an autoimmune condition [11, 12]. However, disruptions in gut microbiota are also now thought to play a major role [13, 14, 11].

Out-of-balance gut bacteria can increase intestinal permeability [15, 16, 17], which causes a cascade of inflammation and an overzealous immune response. Increased intestinal permeability (a leaky gut) is thought to be particularly closely related to the development of autoimmune disease [18, 19, 20, 21, 22]. 

When you remove inflammatory foods, as happens in the AIP and other elimination diets, inflammation decreases, which may help to heal your gut lining and calm your overactive immune response.

In addition to dietary changes, you can give yourself a helping hand by taking a well-formulated probiotic supplement. Probiotics have been shown to: 

  • Help reduce intestinal permeability [23, 24, 25]. 
  • Promote a healthy immune response in your gut [26, 27, 28].

Probiotics are natural helpers for autoimmune patients. For more on how to use them, see our Probiotics Starter Guide.

The AIP Diet is Worth a Try

If you have an autoimmune disease and haven’t seen any symptom relief from a basic elimination diet like the Paleo diet, the autoimmune protocol diet is a worthwhile option. It’s been shown to reduce symptoms and improve quality of life for inflammatory bowel disease and autoimmune thyroid disease patients.

Try the AIP diet for beginners with confidence by keeping things simple, creating a simplified meal plan, and preparing your pantry. Only stick with the diet after the first several weeks if you’re seeing symptom improvement. If you’re doing the AIP diet for Hashimoto’s, you can find more specific help here.

For more individualized help with autoimmune conditions, you can book an online or in-person consultation at the Ruscio Institute for Functional Health.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

➕ References

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