Written by Dr. Michael Ruscio, DC on April 22, 2022
Written by Dr. Michael Ruscio, DC on April 22, 2022 — Reviewed by Aimee Gallo
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.
Autoimmune conditions include:
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:
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.
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.
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).
| Fine to Eat | Avoid at First |
| Nose-to-tail grass-fed or wild-caught animal proteins, including meat, fish, fowl, organ meats, and bone broth | All 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 milk | All 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 melon | Nightshade 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 kimchi | All dairy products, including ghee, kefir, milk, cheese, and cream |
| Herbs and spices not derived from seeds, such as cinnamon, turmeric, thyme, oregano, basil, and rosemary | Spices derived from seeds, including fennel, cumin, dill, anise, mustard, coriander, and nutmeg |
| Stevia and maple syrup | Most 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.
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.
Making any diet change can feel overwhelming and challenging at first, so to make the AIP diet for beginners easier, try these few tips:
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:
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.
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.
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.
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:
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:
Probiotics are natural helpers for autoimmune patients. For more on how to use them, see our Probiotics Starter Guide.
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.
Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.
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