AIP Diet: What It Is and How to Personalize It for Best Results

AIP Diet: What It Is and Specific Steps for Personalizing It for Best Health Results

by Laura Beth Schoenfeld, RD

Last updated on

Reviewed by Tracey Long, MPH, RDN

A strict Autoimmune Paleo Protocol diet isn’t necessary for many people with an autoimmune disease. Find out why.

AIP Diet
Personalizing your AIP diet could allow you to eat foods that are typically prohibited, like peppers. iStock/vanillastring

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? Check out this article to find out. #AIP #paleo #wellness

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
  • Liver
  • 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:

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.

AIP Diet
Adding nutrient-dense fatty fish to your AIP diet could help your body heal from autoimmune disease.

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:

  • Liver
  • 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

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

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. AIP Reintroduction Stages: Take a Systematic Approach

The benefits of reintroducing non-AIP foods are three-fold:

  1. You may be able to tolerate nutrient-dense foods like eggs and dairy, which may improve your body’s ability to heal.
  2. 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.
  3. 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.

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

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

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.)

Avoid Toxins

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 testing and/or pharmaceutical intervention, I strongly recommend finding a qualified Functional Medicine practitioner to work with, such as the ones 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.

Some people with autoimmune disease need to follow a strict AIP diet—but for many with an autoimmune condition, that’s not necessary. They may find, while working with a dietitian or nutritionist, that they’re able to tolerate some foods, while others exacerbate their condition.

Understanding which foods help and which ones harm is just one step in the healing process. The next step? Working with a health coach who is able to help their clients implement the changes a practitioner recommends.

Health coaches are experts at offering support and empowering people to make sometimes difficult changes. Those changes could include letting go of some well-loved foods or adopting different daily habits that will better support immune health.

The ADAPT Health Coach Training Program teaches coaches the skills they need to support their clients as they make those changes happen. We also delve into core concepts of Functional Health, including the diet variations like AIP.

Health coaches are an important part of any collaborative healthcare team—which is one of the reasons why the career is continuing to grow. Learn more about what health coaches do and find out whether this could be the right career path for you with the ADAPT Health Coach Training Program.

164 Comments

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  1. Hello, I have recently been thrown in the BFS camp. Do you think this would help someone like me? And my biggest question is, how do I know if I can or cannot tolerate something? At this point, I don’t have many issues except for constant twitching all over my body.

  2. Hello, I have recently been thrown in the BFS camp! I have done other testing and am so far clean that way. But I would love to reset my body! Do you think this would work for someone like me?

  3. Not to be off topic BUT I have searched high and low for blogs and websites focused on Sub-clinical Hyperthyroidism Grave’s Disease and haven’t found any. I seem to be the opposite of what is described in many hypo sites except for the fatigue, exhaustion, hair loose and other yada yada symptoms.
    I know not as many suffer with hyper vs hypo diagnosis but it can be just as debilitating.
    If you have any advise for a nearly nonexistent TSH yet high T3, T4 people please pass it along to me..I am a poster child!
    Thanks Dana. …aka mother of 6 🙂

    • Hi Dana,

      I have been struggling with the same issue as you for the past 8 years. And unfortunately, I have found little information for sub-clinical hyperthyroidism or good explanation for low TSH and high T3 / T4. While I don’t have any advice for you, I would like to say that I understand what you’re going through and if I come across anything I will post it to this thread.

      • Thank you! I have found a good doctor who finally listens to my symptoms and through deeper tests…I have been diagnosed with Graves Disease. I am being treated with anti-thyroid meds. and feel much better.
        I am a self proclaiming workout addict and I knew something was seriously wrong…my heart rate would go through the roof and all I did was walked up a flight of stairs….so anaerobic became my everyday nightmare and all that it causes. That is so much better….
        Here’s is a little info and a website I found… 🙂
        http://www.mayoclinic.org/diseases-conditions/graves-disease/basics/definition/con-20025811

        Graves’ disease is an immune system disorder that results in the overproduction of thyroid hormones (hyperthyroidism). Although a number of disorders may result in hyperthyroidism, Graves’ disease is a common cause.

        Because thyroid hormones affect a number of different body systems, signs and symptoms associated with Graves’ disease can be wide ranging and significantly influence your overall well-being. Although Graves’ disease may affect anyone, it’s more common among women and before the age of 40.
        Symptoms include….
        Common signs and symptoms of Graves’ disease include:

        Anxiety and irritability
        A fine tremor of your hands or fingers
        Heat sensitivity and an increase in perspiration or warm, moist skin
        Weight loss, despite normal eating habits ( personal note here…I gained weight due to anaerobic fatigue and needing to eat everything, including the kitchen sink, to feel better) lol
        Enlargement of your thyroid gland (goiter)
        Change in menstrual cycles
        Erectile dysfunction or reduced libido
        Frequent bowel movements
        Bulging eyes (Graves’ ophthalmopathy)
        Thick, red skin usually on the shins or tops of the feet (Graves’ dermopathy)
        Rapid or irregular heartbeat (palpitations)

        Hope it helps! Blessings Dana 🙂

  4. Hi Laura – thank you for this weath of information. I have been suffering for 2 years now with eczema, extremely itchy and swollen yets, anxiety, food interolerances (eggs, gluten, dairy), high levels of mercury abd high levels of B12 and B6 which all presented after the birth of my son. I’ve been strictly GF, egg free and DF now for 2 years and while my syptoms have significantly improved I do get flairs at least twice per year. I also take an array of supplements daily inlcuding: Betaine/HCL, Krill Oil w/Evening primrose, muilt vitamin, Vit D3, l-glutamine, zinc, probiotics, B12 (methylated) and methylfolate (I was also taking Milk Thistle but stopped 6 months ago). I’ve recently gone Paleo (2 weeks) to see if this will help and have noticed I have so much less energy (especially around 3pm). My intergrated dr thinks that healing the gut is key. My question is – how long does this typically take to heal and are you suprised that I am not fully healed after almost 2 plus years? When can I start to re-introduce foods like eggs?

  5. I have tried an elimination diet before under medical advice but go into severe withdrawal from carbohydrates all together is there any suggestions for helping with this and getting through it………I experience vomiting shakes and weakness symptoms which often leads me to going off the diet

    • Um. Don’t go off all carbs?
      If your Drs are advocating a ketogenic diet then the brutal fact is you can’t do it, but there’s no reason in the world that you can’t do a reasonably high-carb version of AIP. Taro, plantain, malanga, sweet potato, fruits, cassava. I get 150-200 g carbs a day from those sources, and if I needed to I could hit 300.
      What kind of “elimination diet” have they been trying to put you on that you were not able to get enough carbs?

      • I get ny carvs from sweet potatoes and plantains. They are excellent. You can try butternut squash, too.
        My symptoms are all gone!
        I have 3.5 years grain and gluten free and feel awsome.

  6. Would taking a liver supplement (dried liver in a capsule sold as a supplement) be just as effective as taking it in as a whole food ? Thank you!

  7. First question: I’ve left this comment at a couple other AIP types, but so far no one has responded.
    Part of the AIP philosophy seems to be a horror of seeds. You can’t even sprinkle a little cumin on your food, according to some interpretations. And yet everyone recommends eating seedy fruits with impunity. Figs, raspberries, you name it.
    So… Is there some kind of theory that no one is telling us as to why fruit seeds are different from other seeds? Or has not a single other person in the AIP blogosphere noticed that those lumpy things in fruit are seeds?
    Second question: I can see the argument for “keep doing it until you get results” if you have a confirmed auto immune condition, but what I have is moderately-debilitating chronic fatigue. I’ve been doing it for 3 weeks and am if anything more tired because I spend all of my previous resting time preparing meals. How much longer should I wait for results before I fold?

    • An update, as long as I’m here. On day 28 I got a burst of energy. Not huge, but I no longer need to lie down for 15 minutes after my leisurely walks of the neighborhood, so I’m keeping with it for a while longer.
      I got another big bump in energy when I decided to start prioritizing sleep. Before I was prioritizing not getting hooked on sleeping aids, which meant I got 3 hours several days a week. And since I didn’t seem to have any less energy those days than the days I got 10 hours of sleep, and since the relationship between how long I spent in bed and how long I spent asleep was pretty casual, I didn’t try that hard.
      But I’ve been being more aggressive and wide-ranging in my sleep aids, and just take something when I get up in the night, instead of lying there waiting to fall asleep until it’s too late to take anything else. And more conscientious about being in bed at a decent hour. And I’m feeling better again.
      Still nothing like what I was before I got sick. But certainly more functional.

      • Yay! Yay! and, Yay!!!

        I now, am on that EXACT SAME ROAD to better, more consistent and healing sleeping patterns…Your post is an inspiration! Thank You!

    • Alicia, I had the same question about seeds. I asked on two different websites (The Paleo Mom, and Phoenix Helix), and then later did find the answer in Paleo Mom’s book. Here is the answer from Phoenix Helix: “Seeds within fruits and veggies are fine to eat on the AIP. The reason is two-fold: (1) They are moist and digest more easily than dried seeds. (2) They are a small part of the vegetable/fruit, and if you saw my AIP Food Pyramid, you see that its foundation is vegetables. We don’t want people to exclude them unnecessarily, because their nutrition is very important for healing. The woman who commented above is the exception. Most people tolerate seeds in fruits and vegetables with no problems, so eat them without worries.” – See more at: http://www.phoenixhelix.com/2013/05/19/what-is-the-paleo-autoimmune-protocol/#comment-29922
      The answer from the Paleo Mom was basically the same, but also mentioned that the small edible seeds of fruits tend to pass through undigested.
      Hope this helps!

      • That explains why to eat raspberries, which are easily 30% seeds by dry weight, or figs, which are 60% seeds by volume, even if at least some fruit seeds are loaded with the phytate and lectins that are supposed to be the number one cause of death in the US, according to the more science-impared end of the paleosphere.
        But why shouldn’t I use cumin in a dish that will be 0.5% seeds by weight? Especially if I cook it for a while and then let it hang out in the fridge over night so that it is ‘soft.’
        I think I wrote my question inside out. The question was less “if I can’t eat spices why can I eat fruit” than “if I can eat fruit, why can’t I eat spices,” at least if I use a light hand with them.
        As far as I have seen on any AIP website, the only rationale for eliminating seed based spices is that their very seed-ness makes them devil spawn, so that even a quarter teaspoon once a day would render your entire AIP experiment a waste of time. To me that doesn’t make sense, and triply doesn’t make sense when eating fruit seeds by the tablespoon, and I’m still waiting for someone to explain to me why it would make sense for me to do that.

        • Alicia, no cumin as it’s a nightshade. What others seed based spices are not recommended?

          • The blogs I’ve read have said to eat no seed spices. No pepper, no fennel, no fenugreek, no nothing. And I have not seen any blogs that list cumin as a night shade. In fact, many list it specifically as a non-nightshade safe spice.

              • Seed based spices tend to be common allergens for autoimmune people and can cause systemic inflammation. I have eliminated most seed based spices from my diet because of reactions I have had to them, and later found out I am allergic to many of them and also the autoimmune protocol recommends eliminating them–but AIP is supposed to be temporary, not forever, just to allow the body to calm down and start healing and get to a point where it doesn’t react to everything.

    • Sarah Ballantyne answers this question in her book in Chapter 2 I believe. Small seeds like strawberrys are meant to be eaten whole, it’s when they are broken up that the phytates are released? Any seed that needs to be chewed should be avoided (so she recommends seeding cucumbers). Spices are different, many are nightshades I believe.

    • I will pipe in and respond since nobody else has. If you were looking for answers from Sarah Ballantyne aka the “paleo mom” (supposedly the expert on the protocol), you likely won’t receive much, since she seems to have gone AWOL amidst a flurry of questions. Not very professional IMO, considering her all-or-nothing approach with this whole AIP thing.
      My guess as far as seeds go is that it’s mature seeds that have been given a chance to fully develop, dry and form irritating compounds that are off-limits during the 30-day elimination. But that said, Ballantyne doesn’t allow unripe leguminous vegetables during the elimination phase (snap peas etc), and they’re not ripe. So who knows.
      As for feeling worse during the AIP, I’m in the same boat. I was constipated, worn out and depressed during most of it. I developed mild skin patches on my face that were never there prior, anf when I caught a cold it took me three weeks to heal – which has never happened tome – not even close.
      The bloggers will tell you that it’s you that’s doing something wrong, but as a skilled cook, I was preparing very good meals that were very nutritionally sound, as per their recommendations – plenty of veggies, leafy greens, fruits and carbs in moderation, healthy fats, offal, bone broth, sauerkraut and more.
      Like you, my main issue has been some moderate fatigue along with poor mood. I wonder if perhaps this diet is ok but too difficult emotionally as well as stressful and draining. I also wonder if it’s lacking stimulating foods. Sure, you can eat ginger/cinnamon/cloves/turmeric, but maybe all in all our diets, especially when paired with so much protein, should have more compounds that get you going. I say this because when I reintroduced black pepper, I got mild gut issues, but my bowels went completely back to normal. Maybe the gut “issue” was just peristalsis getting kickstarted, and perhaps reintroducing any stimulating food after strictly omitting it for a month can cause a “reaction” that is natural.

    • Realized after posting (whether it will be reviewed or not I don’t know) that others had replied, just further down. However, I still find the whole seed thing a bit dodgy, and the AIP in general seems to have a lot of loose ends…but if it helps some people, that’s great. I’m always open to improving health through diet/lifestyle, but am skeptical of sef-proclaimed “experts” on the internet.

  8. Laura, if i were to start an herbal round to treat sibo (Dysbiocide and FC Cidal (by Biotics Research)), would I take probiotics or only after the 4 weeks of treatment is over? Are there certain strains to avoid or certain strains that are preferred, i.e. Saccharomyces Boulardii? Thanks!

  9. Thanks for all your info and the excellent presentation.
    Regarding liver: I am in my late 70’s and when I developed pernicious anemia at the age of 4, the “cure” was raw steer (not calf) liver bathed in red wine. It was harder on my Mom than it was on me, but now I CANNOT eat liver plain. However I can eat it in pates. How much nutritional punch am I losing? I have vitiligo, by the way.
    Thank you so much again.

  10. Hi Laura,

    Great post! It’s super in-depth and a truly informative read. Curious as to your opinion – if someone gets a food sensitivity test done and it shows that they’re intolerant to foods, do you treat that the same as a food allergy (i.e. complete avoidance)? Does that most likely mean that you body isn’t designed to tolerate that food, and quite, possibly never will be?

    • Thanks Kayla!

      Food intolerances are different and if leaky gut is completely healed, a person may be able to tolerate those previously intolerable foods in the future. Usually it has more to do with gut integrity, than “not being designed” to handle that food. Allergies that produce IgE antibodies generally cannot be overcome, particularly if they cause an anaphylactic reaction.

  11. Thanks for the great article. Quick question: can taking gelatin as a supplement cause headaches and if so why and can anything be done to prevent them while still taking gelatin? I can eat homemade chicken soup without a problem, but when I have supplemented with pure beef gelatin, after a while, I get daily headaches. The company says there is no hidden MSG, which was my first suspicion. I spend a lot of time cooking already and homemade bone broth just becomes too much…I’d like to cut that corner by taking gelatin but can’t seem to due to the headaches. Any ideas? Thanks!

    • Are you using hydrolyzed gelatin? Either way, powdered gelatin is somewhat high in glutamate (an amino acid) which is the same thing that’s in MSG. So if you’re super sensitive to MSG, you may not be able to tolerate powdered gelatin unfortunately.

      Have you tried eating it in the form of homemade jello? I’m wondering if some of the free glutamate gets bound to other proteins in that situation. It’s worth a try! (And it’s delicious too!)

      I make mine with herb tea and honey.

    • Let your crockpot do the work. I make my bone broth in a crockpot, pour into a muffin tin, freeze, then tip out into a zip lock bag or put in ice cube trays for ease of measuring. I pour out and add water every day for 3 days, then replace the bones. I find I don’t have to monitor the bone broth this way.

  12. Hi Laura,
    My daughter and I did an elimination diet last year. I have Hashimotos, and my daughter struggles with a myriad of minor health complaints (head-aches, stomach aches, acne, bad periods, etc.) We had just bone broth for three days, and then re-introduced foods from there. I am not sure we waited three whole days before trying our next foods, and I did not think to worry about nightshades.
    Nothing conclusive resulted with me, but immediately my daughter reacted to eggs and to peanuts with gastrointestinal symptoms. I have two questions.
    1) While my daughter complied with eliminating eggs and peanuts for a time, she re-added them to her diet without gastrointestinal problems. I do not understand this. How could the symptoms be so immediate and obvious one day, and then almost like a mind over matter, not be evident at another time?
    2) My daughter still has all the same health issues. I suspect that she has a dairy issue that may cause her headaches on subsequent days. She has agreed to do some blood tests to put the matter to rest. I had previously heard of Alcat tests. Are these a similar test? What would you prefer and why? We are outside Toronto, in Ontario, Canada.

    • Hi Jean. I would suspect that foods like eggs and peanuts are contributing to some gut permeability (aka leaky gut) and when she avoids the foods for long enough, the gut heals and can tolerate an occasional exposure more easily. Your daughter may benefit from one of the food intolerance tests. ALCAT is one that many of my colleagues recommend. I personally like Cyrex’s Array 4 and/or 10, and other RDs that I know offer something called LEAP testing that has given their clients good results.

      It really just depends on what you’re able to get done. I’m not sure which of those tests would be available to you in Canada.

      But I’d focus on getting her on a gut healing diet, which may require eliminating dairy for at least 30 days. It sounds like she has some hormonal imbalances which can be exacerbated by poor elimination.

      And I’d suggest finding a practitioner to work with so you’re not spinning your wheels for months on end!

  13. I have CD and Hasimoto’s. I’ve been off of gluten for a couple of years but still have issues. I am also UNDER weight so I have to be careful on elimination diet. I tried a couple of years ago and was weak and lost too much weight. Last week, I just started the 30 day reset and I’ve been off all dairy, legumes, grains, chocolate, nightshades, corn. I am still eating eggs at this point because I was tested once and it came up negative. Also, I don’t seem to have a problem but if after 30 days, I’m still not feeling a lot better, I may consider it. I have to be very careful not to lose weight like last time. I am also cutting back a lot on sugar intake. No refined sugars. Some fruits and some blueberry bread that I make out of coconut flour adding a TBSP of raw honey. I’m going to see how I feel after 3 more weeks on this diet.

  14. Just curious, do most of us still say we’re on AIP even after successfully reintroducing some of the eliminated foods? I left an AIP online group because there was so much contention about whether AIP was only the elimination phase (no reintroduced foods) or included “thereafter” for those who were later tolerating eggs, nuts, etc. Those who mentioned eating those foods were reminded that it’s not AIP. I wanted encouragement to pursue my personal modification after reintroduction.

    • I’m not sure if you should say you’re on AIP specifically but perhaps saying that you went through the AIP protocol is more accurate.

      For the sake of not confusing newbies, I’d be sure to make a note that foods you reintroduced were not strict AIP.

      PS – I’m not sure why people would not be encouraging to those who went through the whole process… but the online world is often weird to me. 🙂

  15. it’s just an elimination diet. maybe there wouldn’t be so much confusion if you would just call it that instead of trying to come up a brand name.

    • or maybe she would like to differentiate it from other “elimination” diets so as not to be confused with said diets because it undoubtedly has aspects that are unique. surely you have something better to do with your time than nitpick the name of a diet?

    • Like Jonathan said, it’s a specific type of elimination diet geared towards those with autoimmune diseases.

      Similar to a Low FODMAP diet which is still an elimination diet but it’s geared towards people with IBS and other GI issues.

      Not sure why naming it in a way that helps people pick the right foods to try eliminating is an issue.

  16. Thank you so much for this article! I am going to start Paleo ASAP. I was diagnosed with Chronic Fatigue, Fibromyalgia, IBS, and severe idiopathic neuropathy. Psoriasis has been part of my life since my teen years (30 yrs), so I know I have had AI problems most of my life. I have been on disability for about 4 years now after trying desperately to continue working for a few years. I am still mostly bedridden due to the severe neuropathy and fatigue. My journey has lead me to natural health and the hopes of complete healing. Every day I try to search and learn more about health and what I might do to heal. Fibromyalgia symptoms have been in remission for a little while. I am just beginning some fermented foods- mostly kombucha and kefir. I have lost a significant amount of weight due to a cdiff infection and though the infection is gone, I’m continuing to lose weight in my effort to reduce portions and eat high protein/low carb. (I still have a lot to lose… though my main concern is complete health.) Neuropathy is the most difficult part of my life… the pain is daily and can be excruciating. So my question… have you worked with anyone with idiopathic neuropathy and had success in remission? Do you believe Paleo would help me??

    • Hi Brenda

      Just a few tips that might help.
      Your FM is likely related to low thyroid hormones and you need to get a full thyroid function test including reverse T3 done. Check out this article by Dr John Lowe who did a lot of research on the connection
      http://www.thyroiduk.org.uk/tuk/related_conditions/Fibromyalgia-medical-mystery-solved.html

      You really need to find yourself an integrative medicine doctor to do the full thyroid test but you can also test your basal temperature (your temperature when you first awaken and before you move around) in your armpit. If low, it is an indicator of low thyroid hormones or inability to use them effectively. See this article on how to do it but I do recommend doing it in the armpit only and preferably using a mercury thermometer
      http://www.stopthethyroidmadness.com/temperature/

      Also, I strongly suggest taking Magnesium Citrate for your peripheral neuropathy which BTW, may also be caused by low thyroid hormones. Not only will the magnesium help reduce the inflammation but will also relax your muscles and improve your energy. You can order Life Extension Magnesium Citrate inexpensively from iHerb. (This form is the most efficiently absorbed and really is worthwhile getting as opposed to other forms – don’t get tablets as your digestion is bound to be very poor and you will waste your money). Start slowly with 1 capsule morning and night and increase every few days by 1 cap up to 4 caps per day – you can put it in your water bottle to reduce the risk of loose stools. If you do get loose stools then back the dose off to the highest you can tolerate without that happening. Another way of possibly increasing your magnesium level faster is by using magnesium “oil” which is not really an oil at all, however Professor Vormann, a world renown magnesium expert denies that we can absorb magnesium through the skin. He does however say that it may help to reduce the body’s acidity if you soak in an epsom salts bath (use 1-2 cups in a bath).

      Also, peripheral neuropathy is sometimes caused by vitamin B12 deficiency. If you do have an autoimmune thyroid problem you possibly also have autoimmune destruction of your parietal cells that line your stomach and you should speak to your doctor about being tested and trialling B12 injections if you are deficient.

      • Thank you for responding to my comment!
        I have had several thyroid tests, including rT3 and rT4. My MD and my NMD did not find the results significant. However, I was on NaturThryoid for a couple years, with no results. I do continue to have a low basal temp.
        I discovered, while fighting Cdiff, that I am extremely mineral deficient… especially in magnesium. Now that Cdiff is gone, I continue to need large doses of magnesium (I’m using Natural CALM) day and night just to keep my heart healthy. One day without it and I have migraines, racing/pounding heart, worsened pain, and no sleep. Clearly there is a mineral problem, but as I have changed my diet severely, I can not figure out why my body will not hold minerals- especially magnesium. I did find that my digestion won’t process capsules, so I must take it in liquid. I also do Epsom baths and magnesium oil… both are not enough to function properly. I did take B12 for a long time too, with no results. I’m thinking that if my body won’t absorb the magnesium then perhaps it isn’t absorbing the other supplements either. I have not found a reason that my body isn’t absorbing nutrients. Any ideas?

        • Hi Brenda,

          Leaky gut, which is increased permeability of the intestinal wall, can cause poor nutrient absorption, and has been found to co-exist with most autoimmune disorders.

          I also have Fibro and small fiber neuropathy, and I’ve found that Magnesium Malate helps some and doesn’t give me gastrointestinal issues like Magnesium Citrate does. I’ve also heard good things online about benfotiamine for neuropathy.

    • One more thing Brenda – have you been tested for H pylori? That could be another cause of low B12, and low stomach acid, which in turn hampers your protein digestion and mineral absorption, as well as other aspects of your digestion and can set you up for a whole range of problems in your small and large bowel (bacterial imbalances, infections, parasites etc).

      Hope this helps.

    • Hey Brenda, Kris had some great points for you below. I agree that getting more B12 into your diet (or taking shots) is a good place to start.

      With the complexity of your situation, I do think working with someone directly would be helpful.

      I’m happy to discuss your situation and determine if my services would be a good fit for you. Feel free to book here: http://lauraschoenfeldmphrd.satoriapp.com/book

    • Psoriasis became a nightmare for me at age 14, the same time I was diagnosed with Ulcerative Colitis. Now I am 58, have been doing Paleo AIP, low fodmap for about 2 years now. Each time I try to add food back in I seem to return to the psoriasis on my face pretty quickly or I get joint pain when I try to add nightshades. I have come to the conclusion I will probably be on a pretty strict diet for the rest of my life. Am I unhappy, NO! I am thrilled to have found a space to be comfortable in. Another benefit is I no longer have bloody diarrhea, so I am betting my next colonoscopy shows healing as long as I behave myself on the diet. The new recipes I have discovered far surpass the old recipes in flavor, so I have new comfort foods. My cranberry upside down cake is wonderful, non AIP friends have no clue and I don’t tell them because they think the cake tastes great. I make homemade coconut milk and horchata ice cream folks also love. Might take awhile to find recipes for yourself, but I think you will be delighted when you do.

  17. Hi Laura, thank you for a great article. I was diagnosed with Hashimotos in March and got a functional doc that diagnosed me with an h. Pylori infection last May. Based on my history it is possible I have had the h. Pylori infection since I was a teenager (I am in my 40s now) I went through a treatment of antibiotics for the infection in May, and then again recently and am having a tough time getting rid of the infection. It is hard to tell which if my symptoms are from Hashis and which are from h pylori. I had leap testing last May done by a nutritionist and some of my highly reactive foods were chicken, beef, shrimp, peppers, cucumbers and some of my extremely low reaction foods were eggs, tomatoes and cocoa. Dairy fell mid range. I have been off Gluten for a year and off soy protein since April. What would you do under these circumstances? I feel like my h pylori has my intestinal system so messed up that everything I eat makes me sick.

    • Are you using HCL or digestive enzymes? You may have low HCL which means you’re not fully digesting proteins as well as you should be. That’s a common symptom of h. pylori because it shuts down your stomach acid production.

      There are also some natural supplement options for reducing h. pylori.

      Please feel free to get in touch with me if you think nutrition counseling might benefit for you. You can sign up for a free consult and we can discuss your case: http://lauraschoenfeldmphrd.satoriapp.com/book

    • Have a look at the diets that were ranked ahead of paleo and then ask who would benefit from these diets being higher ranked? Clue: not the sweet potato, fermented food and bone broth providers.

    • When you read the description of the “paleo” diet that they used to judge it, it becomes clear why it tested so badly. I don’t remember the details, other than that it was aggressive IF, which isn’t good for everyone, but it was pretty crazy. I don’t remember if it was low cal or low fat or didn’t mention veggies or what, but it really was a terrible diet. Just it wasn’t, you know, what anyone in the paleosphere means by “a paleo diet.”

  18. Hi Laura,

    I’m really stunned what the Paleo diet has to offer.. I have a great passion for food and cooking. I’m always thinking of what i am cooking tonight.. The Paleo cookbook has definitely helped me finding out new (and more importantly) healthy recipes!

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