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The Autoimmune Paleo Protocol diet (also known as the Autoimmune Protocol, or AIP, diet) is a fantastic way to start seeing a vast improvement of autoimmune disease symptoms. However, the major issue I see frequently is that once someone has seen success on a strict AIP diet, they’re often afraid to try adding back in any foods that are eliminated from the diet.
One thing that many people don’t understand about the AIP diet is that not everyone with an autoimmune disease needs to be on this diet indefinitely.
In fact, only a few people with autoimmune diseases need to strictly and permanently avoid all the foods eliminated from the diet, as not everyone with autoimmunity is intolerant to all these foods.
My goal when I work with clients is to get them on the least restrictive and simplest diet possible that provides the most amount of health and vitality. While those with an autoimmune disease generally have less wiggle room than the average healthy person, it’s important to remember that the AIP diet need not be followed strictly for the rest of one’s life.
In this article, I’ll briefly cover the five major steps to personalizing your AIP diet, in order to have the most flexible and health-promoting diet possible.
If you have an autoimmune disease, you’ve likely heard of the AIP diet. But do you know how to personalize it and, potentially, reintroduce foods that you once had to avoid?
What Is the Autoimmune Protocol Diet
The goal of the AIP diet is to remove foods that could trigger inflammation or harm gut health and instead eat nutrient-dense foods that promote health, like:
- Bone broth
- Fermented foods
- High-quality meats
- Leafy and cruciferous vegetables
- Healthy fats from whole plants and animals
Based on a general Paleo template, the AIP diet focuses on removing foods like:
- Industrial seed oils
- Refined sugar
- Nightshades (like eggplants, tomatoes, and potatoes)
The AIP diet routinely gets a lot of attention, even in the mainstream media. Some question if the diet is a legitimate way to manage autoimmune disease, asserting that “a lot of it doesn’t make much biological sense.”
However, advocates of the diet, particularly Dr. Sarah Ballantyne (known as “The Paleo Mom”) and Dr. Terry Wahls, have provided heaps of evidence, both peer-reviewed and anecdotal, that the diet does indeed help those with autoimmune disease not only manage their symptoms, but even begin to reverse the disease, or at least halt its progression.
As a dietitian, I’ve seen incredible results with clients who were able to successfully implement the AIP and eliminate many of their symptoms, whether they were suffering from Hashimoto’s disease, Sjögren’s syndrome, psoriasis, rheumatoid arthritis, multiple sclerosis (MS), and more. It’s amazing to see a person’s health turn around after implementing the diet change, especially when the disease they’re dealing with had been taking so much of their quality of life away from them.
But as I mentioned above, the introductory AIP diet is highly restrictive, and for some people with autoimmunity, it doesn’t need to be followed forever. That’s why it’s so important to take steps to personalize your AIP diet.
1. Start with a 30-Day Reset
In Chris Kresser’s book The Paleo Cure (formerly Your Personal Paleo Code), he suggests that everyone looking to discover their ideal diet start with a 30-day strict Paleo protocol. This means following the standard Paleo guidelines: no grains, no dairy, no legumes, no industrial seed oils, no alcohol, and so on. I suggest that someone with an autoimmune disease who is currently eating a standard American diet start with the normal Paleo 30-day reset.
Many people with autoimmunity will do just fine following a Paleo diet, and adding in the autoimmune diet restrictions shouldn’t be necessary in this situation. Going immediately from a standard American diet to an AIP can be overwhelming for many people, which is why I generally suggest starting with the standard Paleo approach if you haven’t done so yet.
That said, if you have already given the standard Paleo 30-day reset a try, or perhaps you’ve been strict Paleo for many months, and your autoimmune symptoms haven’t decreased significantly, consider trying another 30-day reset. This time, I recommend adding in the standard AIP diet restrictions, as well. This means additionally eliminating eggs, nightshades (e.g., potatoes, tomatoes, eggplant, peppers), and nuts and seeds.
Sticking to the diet for a minimum of 30 days gives your body a chance to begin calming the autoimmune response, healing the gut lining, reducing inflammation, and repairing damaged tissues that were subject to the autoimmune attack.
I generally recommend extending the reset to a minimum of 60 days for people with severe autoimmune conditions that affect neurological function, or cause symptoms that have a noticeable impact on daily life. I’ve found that most people see enough improvement within the first 30 days that extending the reset another 30 days is no problem for them.
And remember: every time you eat a food that triggers an immune response, such as gluten, dairy, eggs, etc., your body produces antibodies that incite an attack on your immune system. This autoimmune attack can last for days, weeks, or even months if the intake was significant enough. Committing 100 percent to the reset time period is crucial for a person with an autoimmune disease to see the improvements they’re looking for.
It’s important to acknowledge that an AIP diet is not a cure, and it may not be enough to put a disease into full remission or heal damaged tissues. Further support such as medication or targeted AIP supplements may be necessary to maintain the body’s optimal functioning. There is no shame in using conventional medicine in addition to a dietary and lifestyle approach to healing.
That said, by removing the foods and toxins that contribute to the autoimmune response and providing adequate nutrients to fuel the healing process, you can significantly reduce symptoms and even possibly put the disease into remission.
2. Optimize Your Nutrient Intake
Speaking of adequate nutrients, simply removing foods from your diet isn’t enough to heal from an autoimmune disease. You need to be purposeful about adding certain foods into your diet to provide the nutrients and building blocks your body needs to repair damaged organs, modulate the immune system, and heal the gut lining.
In addition to removing the common autoimmunity triggers listed above, it’s essential to add in nutrient-dense foods like:
- Bone broth
- Large amounts of colorful vegetables
- High-quality meats and fats
- Fatty fish and shellfish
- Fermented foods
I’ve worked with clients who were following the AIP restrictions consistently, but they’d forgotten to add in some of these nutrient-dense foods, which meant that their ability to heal wasn’t optimally supported.
Another unexpected benefit of focusing on adding foods is the impact your total calorie intake will have on healing. In this interview with Eileen Laird, I explain the very common challenge many of my clients following the AIP diet face: undereating. With the number of restrictions on a strict AIP diet, it’s very easy to fall into the trap of not eating enough total calories. And no matter what your health challenges are, chronic undereating is a recipe for worsened health.
Be sure to emphasize adding more of the following foods, along with eating enough total calories, as you work to heal your body from any autoimmune disease.
Liver, Fatty Fish, and Shellfish
Nutrients in liver, fatty fish, and shellfish such as vitamin A and D, zinc, choline, and various B vitamins are essential for modulating the immune response (particularly the T-regulatory cell response), supporting mitochondrial energy production, and supporting the healing of damaged tissues, especially the gut lining. (1, 2, 3, 4, 5) Liver is especially important to eat when on a strict AIP diet, as it contains nutrients that would otherwise come from eggs, which are removed on the AIP diet.
Since the current theory of autoimmune disease is that a “leaky” and inflamed gut is required for the development of autoimmune disease, eating a diet that supports healthy gut integrity is of immeasurable importance. (Discussing leaky gut in detail is outside the scope of this article, but if you’re looking for more information on leaky gut, check out this episode of Revolution Health Radio.)
Fermented vegetables not only provide beneficial probiotics, they also contain fermentable fibers that can feed the flora that are already in the gut. A healthy gut microbiome is crucial for maintaining a healthy gut lining, thanks primarily to gut bacteria’s ability to produce butyrate, which is important for T-regulatory cell production and differentiation, and can help further balance the immune system. (6)
Bone broth contains gelatin, a protein that contains the amino acids proline, glycine, and glutamine. These amino acids can help heal the gut lining, reduce inflammation, and promote healthy gut integrity. (7) Glycine, in particular, is known to inhibit immune activity and act as an anti-inflammatory. (8) That’s why bone broth is one of the major dietary staples of a gut healing, anti-inflammatory diet that is ideal for a person with an autoimmune disease.
While many of my clients with autoimmune disease are doing great at avoiding the foods on the AIP protocol, they still often struggle with adding in nutrient-dense foods like liver, shellfish, fermented vegetables, and bone broth. These foods should be considered an integral part of an effective AIP approach, and I strongly encourage those with autoimmune disease to make the effort to add these foods in regularly.
3. Systematic Approach to the AIP Reintroduction Stages
The benefits of reintroducing non-AIP foods are three-fold:
- You may be able to tolerate nutrient-dense foods like eggs and dairy, which may improve your body’s ability to heal.
- You’ll have a better understanding of which foods are more crucial to avoid than others, which can give you freedom in your food choices.
- Having a more broad diet can significantly improve your ability to enjoy food both at home and when out to eat, which provides important quality of life benefits.
Bonus: If you’re able to tolerate dairy, you can enjoy the nutritional benefits of grass-fed dairy. In fact, raw milk may have special benefits to those with autoimmune disease, as drinking raw milk can boost glutathione levels substantially, and glutathione is another nutrient that can modulate the immune response. (9)
Reintroducing foods is probably the most challenging part of personalizing your AIP diet. As I mentioned before, it can take hours, days, or weeks for an immune response to kick in to the point where symptoms return. While some people have an immediate and strong reaction to foods they eat that they have immune activity against (gluten is a big culprit here), others have only minor increases in symptoms that they may not realize are attributed to a particular food.
The best way to construct a reintroduction protocol for an autoimmune diet is to first choose which foods are the most important to you to try reintroducing, and then work systematically to bring them back into your diet. I rarely suggest trying to reintroduce gluten if you have an autoimmune disease, but other excluded foods like dairy, eggs, nightshades, and/or nuts and seeds, and even non-Paleo foods like white rice and legumes, can frequently be tolerated by those with an autoimmune disease.
Certain food groups need to be reintroduced in a particular order. The best example of this is dairy, where you start by reintroducing ghee, which contains the least amount of milk proteins, then continue with other dairy types in this order: butter, heavy cream, fermented dairy (yogurt and kefir), cheese, and fluid milk.
Other examples include eggs, which should be introduced yolk first, and nightshades, which need to be introduced one by one (e.g., first potatoes, then tomatoes, then eggplant, and so on). You can also reintroduce non-Paleo foods like white rice and other gluten-free grains, if desired.
Chris lays out the instructions for the reintroduction phase in his book The Paleo Cure, but the most important thing to remember is to only reintroduce one food at a time, and to give yourself at least three solid days per reintroduction to notice any exacerbations in your symptoms.
This can be a return of your specific autoimmune symptoms such as joint pain or skin inflammation, or it may be a new, “unrelated” symptom like gastrointestinal distress or fatigue. If you’ve eaten the food consistently for three days and you don’t notice any negative side effects, you can generally assume the food is okay for you to eat.
4. Get Tested for Sensitivities
Sometimes, the reintroduction protocol isn’t enough to discover which foods are causing you to have immune system flares. If your symptoms aren’t improving on a strict AIP diet, or if you’ve gone through the reintroduction protocol and your symptoms start to come back, you may still be eating a food that’s inciting an immune response.
In this case, getting food sensitivity testing is a good option to determine exactly which foods are the culprits. I typically see most clients with autoimmune disease getting their testing done through Cyrex Laboratories, which tests for both immunoglobulin G and immunoglobulin A antibodies and can detect intolerances to a wide variety of foods.
They’ve released a test called Array 10, which covers a great deal of foods in both cooked and raw form, and I’d imagine this test would be beneficial to a person on the AIP diet who’s not seeing the improvements they were hoping for. Array 4 is another Cyrex test that I frequently use for clients who are unsure of whether they’re intolerant to dairy, eggs, or other foods that are commonly associated with a gluten cross-reactivity response.
It’s important to note that these tests are accurate only if you’ve eaten the food in question within the past four to six weeks. So if you’ve been dairy-free for six months, testing for a dairy sensitivity likely wouldn’t give you a positive result, even if you are truly intolerant. The testing option is more suited to people who have been eating some of the questionable foods recently and have experienced a return or an exacerbation of symptoms.
It’s also very important to note that many food sensitivity tests are on the market these days, and most of them are questionable when it comes to their usefulness. There are many reasons why I don’t recommend most food sensitivity testing, such as lack of evidence to support their accuracy, as well as the potential for the results to create disordered eating habits in the person taking the test. Not to mention, those tests can distract a person from addressing the root cause of their food sensitivity, and eliminating those sensitivities by healing the body appropriately.
If you feel that you need to get testing done to determine which foods might be an issue for you from an immunological standpoint, I strongly recommend working with a qualified practitioner who can help you navigate the testing options and interpret the results of your tests.
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5. Focus on Your Lifestyle
Even though I’m a dietitian, I find that lifestyle habits other than diet often play an important role in my clients’ health outcomes. It’s always interesting to have someone come to me expecting to take on a diet change, and by the end of our first session, we’ve skipped the diet and gone straight to the exercise, stress, and sleep recommendations.
Unhealthy lifestyle practices can completely undo the benefits of a healthy diet, and examining your habits is an important next step once your diet is taken care of.
Exercise isn’t just great for weight loss and cardiovascular health, it’s also crucial for healthy immune function. Research shows that exercise is important for T-regulatory cell production, and it can also reduce inflammation in people with autoimmune disease. (10, 11, 12, 13)
Daily exercise at a low to moderate intensity is what I typically recommend for people with autoimmune disease. This means:
- Avoiding excessive or overly intense exercise
- Allowing for adequate rest between workouts
- Aiming for daily low-intensity movement
- Limiting sedentary behavior
Manage Your Stress
As Chris explains in The Paleo Cure, chronic stress has been shown to reduce gut barrier integrity (remember the leaky gut connection?) and can trigger or worsen autoimmune disorders including MS, Crohn’s disease, psoriasis, and rheumatoid arthritis. (14)
One study even found that chronic psychological stress is associated with the body losing its ability to regulate the inflammatory response. (15) The researchers theorize that the stress connection may explain why women have a higher prevalence of autoimmune disease than men do.
I completely agree with Chris when he says:
“If you’re not doing some form of regular stress management, you will sabotage all of your best efforts with diet, exercise, and supplements.”
Minimizing stress is non-negotiable for my clients with autoimmune disease. There are dozens of different ways you can manage stress, from yoga, to meditation and prayer, to planned social occasions with loved ones. Petting a dog, getting a hug from a significant other, or getting a monthly massage can all be stress-relieving activities, as well. There are so many ways to reduce stress; the most important thing is to pick a few that work best for you and your lifestyle.
Sleep is another non-negotiable factor in my clients’ autoimmunity management plans. Chronically poor sleep is not only a source of stress, but also a source of inflammation. (16) When circadian rhythms get misaligned from weeks or months of inadequate sleep, inflammatory immune cells are produced excessively, leading to an increase in “friendly fire” against the body’s own tissues.
If you’re concerned about your sleep, check out the recommendations provided in this article, and read Dr. Ballantyne’s excellent post on the role of circadian rhythms in regulating hormone cycles and how to get your rhythms back on track.
Spend Time Outdoors in the Sun
Sunshine is the best source of vitamin D, and healthy vitamin D levels have been shown to directly influence the activity of the immune system. In fact, not only has vitamin D deficiency been connected with a higher risk of developing autoimmune disease, but the vitamin is also used as a treatment for reducing the symptoms of autoimmune disease. (17, 18, 19, 20)
So don’t be afraid of the sun, particularly if you live far from the equator and/or have darker skin! And if regular sun exposure isn’t an option, you may benefit from supplementation. (Work with a professional to determine your optimal dose.)
Finally, avoiding toxins in everyday life can reduce the burden on your immune system. As an example, one study in mice showed an increased risk of developing autoimmune disease when exposed to phthalates. (21) Phthalates are relatively common chemical “plasticizers” that are found in everything from detergents, to building materials, to plastic food and beverage containers, to cosmetics.
You can minimize your exposure to chemical toxins by using natural products for cleaning your house and laundry, drinking out of glass bottles instead of plastic, and minimizing your use of industrial cosmetics. A great resource for DIY cosmetics is Liz Wolfe’s Skintervention Guide, and there are dozens of blog articles about how to clean without using toxic chemicals.
Get Help When You Need It!
By following these five tips for personalizing your AIP diet, I believe the majority of people with an autoimmune disease will see significant improvements in their symptoms.
That said, there are those who will need additional tweaks, deeper testing, and personalized changes to their diet, supplement, and lifestyle plan before they see the improvements they’re looking for.
This is especially true for people with severe gut issues, long-term neurological involvement, or compounding issues like surgical intervention or pharmaceutical dependency.
For those who need in-depth care, I strongly recommend finding a qualified Functional care team to work with, such as the one at the California Center for Functional Medicine.
And for those who may simply need more advice about how to tweak their diet, supplements, and lifestyle to optimize their results on the AIP diet, I’d be happy to help guide you in the right direction.
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