5 Steps to Personalizing Your Autoimmune Paleo Protocol | Chris Kresser
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5 Steps to Personalizing Your Autoimmune Paleo Protocol


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

aip diet
Getting your autoimmune symptoms under control through the AIP diet is key to a happy, healthy life. CentralITAlliance/iStock/Thinkstock

This is a guest post by Laura Schoenfeld, a Registered Dietitian with a Masters Degree in Public Health, and staff nutritionist for ChrisKresser.com. Click here to learn more about her nutrition consulting services.

The Autoimmune Paleo Diet has been getting a lot of attention lately, 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.”

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 patients who were able to successfully implement the autoimmune protocol and eliminate many of their symptoms, whether they were suffering from Hashimoto’s disease, Sjogrens, 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.

While the Autoimmune Paleo Diet is a fantastic way to start seeing a vast improvement of symptoms, the major issue I see frequently is that once someone has seen success on a strict autoimmune Paleo protocol, 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 Autoimmune Paleo Diet is that not everyone with an autoimmune disease will need to be on this diet indefinitely.

In fact, there are few people with autoimmune diseases that would need to strictly and permanently avoid all the foods eliminated from the diet, as not everyone with autoimmunity is intolerant to all of these foods.

My goal when I work with clients is to get them on the least restrictive diet 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 Autoimmune Paleo Diet need not be followed strictly for the rest of one’s life.

A strict Autoimmune #Paleo Diet isn’t necessary for many people with an #autoimmune disease. Via @AncestralizeMe

In this article, I’ll briefly cover the five major steps to personalizing your Autoimmune Paleo Diet, in order to have the most flexible and health-promoting diet possible.

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 believe that someone with an autoimmune disease who is currently eating a standard American diet should start with the normal Paleo 30-day reset.

There are many people with autoimmunity who 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 autoimmune protocol can be overwhelming for many people, and that’s why I generally suggest starting with the standard Paleo approach if you haven’t 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 Autoimmune Paleo Diet restrictions as well. This means additionally eliminating eggs, nightshades (e.g. potatoes, tomatoes, eggplant, peppers), 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 will produce antibodies that incite an attack on your immune system for days, weeks, even months if the intake was significant enough. Committing 100% to the reset time period is crucial for a person with autoimmune disease to see the improvements they’re looking for.

It’s important to acknowledge that an Autoimmune Paleo 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 supplementation may be necessary to maintain the body’s optimal functioning.

That said, if you can remove the foods and toxins that are contributing to the autoimmune response and provide 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, 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, copious amounts of colorful vegetables, high quality meats and fats, fatty fish and shellfish, and fermented foods.

I’ve worked with patients who were following the Autoimmune Paleo restrictions beautifully, but they’d forgotten to add in some of these nutrient dense foods, which meant that their ability to heal wasn’t optimally supported.

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 Autoimmune Paleo (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 unmeasurable importance. (Discussing leaky gut in detail is outside the scope of this article, but if you’re looking for a program to help you through the recommended diet and supplement protocol for intestinal permeability, check out Solving Leaky Gut.)

Fermented vegetables not only provide beneficial probiotics, but also 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 autoimmune disease.

While many of my autoimmune patients 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 diseases to make the effort to add these foods in regularly.

3. Reintroduce Foods Systematically

The benefits of reintroducing non-AIP foods are three-fold. First, you may be able to tolerate nutrient dense foods like eggs and dairy, which may improve your body’s ability to heal. Second, 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. Third, 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 are returning. While some people get an immediate and strong reaction to foods they eat that they have immune activity against (gluten is a big culprit here), others only have 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 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. 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 3 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 an “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 culprit. I typically see most autoimmune patients getting their testing done through Cyrex labs, which test for both IgG and IgA antibodies and can detect intolerances to a wide variety of foods.

They’ve recently 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 that’s not seeing the improvements they were hoping for. Array 4 is another Cyrex test that I frequently use for patients 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 only accurate if you’ve eaten the food in question within the past 4-6 weeks. So if you’ve been dairy-free for 6 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 exacerbation of symptoms.

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 under control.

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’d 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, and limiting sedentary behavior.

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 multiple sclerosis, Crohn’s disease, psoriasis, and rheumatoid arthritis.

One study even found that chronic psychological stress is associated with the body losing its ability to regulate the inflammatory response. (14) The researchers even 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 a non-negotiable for my autoimmune clients. There are dozens of different ways you can manage stress, from yoga, to meditation, to planned social occasions with loved ones. Petting a dog, getting a hug from a significant other, or a monthly massage can all be stress relieving activities as well.

In the 14Four program, we’ve compiled a list of resources for managing stress appropriately, so check out that program if you need some assistance finding a stress management practice that works for you.

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. (15) 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 we provide in the 14Four program, and read Sarah Ballantyne’s excellent post on the role of circadian rhythms in regulating hormone cycles and how to get your rhythms back on track.

Sunshine is the best source of vitamin D, and good 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 it also is used as a treatment for reducing the symptoms of autoimmune disease. (16, 17, 18, 19)

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 pthalates. (20) Phthalates are relatively common chemical “plasticizers” that are found in everything from detergents, building materials, plastic food and beverage containers, and 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 plastics, 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 5 tips for personalizing your autoimmune paleo protocol, 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, longterm 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 integrative doctor or naturopathic physician to work with.

And for those who may simply need more advice about how to tweak their diet, supplements, and lifestyle to optimize their results on the Autoimmune Paleo protocol, I’d be happy to help guide you in the right direction.

Have you overcome your autoimmune disease using any of the recommendations I described above? Share your story in the comments below!

About Laura: Laura uses her knowledge of traditional and biologically appropriate diets to improve her clients’ health. Growing up with a family that practices Weston A. Price principles of nutrition, she understands the foods and cooking practices that make up a nutrient dense diet.

With her strong educational background in biochemistry, clinical nutrition, and research translation, she blends current scientific evidence with traditional food practices to help her clients determine their ideal diet.

You can find her at AncestralizeMe.com, on Facebook, and Twitter!


Join the conversation

  1. Unfortunately a doctor for Functional Medicine is VERY expensive in my country, and i have to pay it all on my own. I am already saving up money, but it will take a time till i can make an appointment. Life sucks.

  2. Hi

    i Have been struggling from a disease named Lichen planus , and now its increasing very rapidly , i am trying AIP now , my question is whether i can drink milk or not ?

  3. Hi!
    I find your website filled with useful information.
    I started with AIP 7 weeks ago and I do not feel any better. I still keep cutting and cutting food from my (now very short list) and I am confused about getting no result. I can’t eat dark green vegetables like kale, broccoli or spinach. I also have issues with bananas and apples. I buy only organic food (vegetables and meat). I need to eat sweet potato or butternut in the evening for getting a good night sleep. Still have bloating, brain fog, skin issues, tired, weak muscles… Every day. Do you have any suggestion for me?

    • Hi, I am not a professional but only have the same experience as you. First I would advice you stop eating meat and meat products for a period of time and see how you feel, allow 7 to 30 days to notice any difference. With apples and bananas, I believe it is because of the carbohydrate and sugar content. May be that is why sweet potatoes and butternut makes you fall asleep, both have a bit high sugar and carbohydrate content as well for someone with food sensitivities. I have slowly transition to raw food, because cooked food barely gives me any energy. It may not be the food, but major inflammation and gut permeability in the gut, causing food sensitivities that you may not react to other wise. Seek a professional to find out your food sensitivities for now. Doing a juice cleanse for a body reset also helps. Also your body needs time to heal, and less food in the gut for it to process helps. I hope this helps and you find the best way to heal, it is a difficult journey, keep you spirits up and have fun.

  4. Hi I was diagnosed with autoimmune thyroidism disease last year. I am on 75g of eltroxin. I have started paleo reset diet. My tongue swells out with indentation on side and I was wondering if this is an indicator of inflamation in the throat. I find my memory not ss good as before. Would I continue reset diet on till indentation is gone or will I just start reintroducing foods after 30 days and stay gluten free. Hoping you can help.

    • I have the same thing. I ate aip for a year for my hashimoto thyrd and attack on my joints. I have reAlized i have strict sensitivity to gluten of course and soy. When i was strict paleo the tongue inflammation was better but Must’ve added the wrong things in. Now I have gallbladder issue going on partly attributed to my strict paleo): I need to eat lowfat diet till gallbladder is removed and better.

  5. I thought I had it bad…Having to lose 60% of hair on my head (AA) and to have itchy, scaly and bleeding from scratching constantly on my back (eczema).

    So many pepole suffer from much worse conditions everyday.

    But each of is suffering in agony just as much as others, just in different ways.

    For me, I know I need to be on AIP but it just sounds like a lot of work. So I’m very discouraged. I’m sure it’ll get easier as you put in more days.

    Good luck to everyone suffering… Hopefully, you’ll regain your health in the near future.

    And remember, don’t get frustrated (from pain or condition/severety of your disease) and take it out on your family or friends. Because they’re suffering, too. (From not having “you” as in real, healthy you.)

  6. Hi. I am only about a week into the AIP diet but every SINGLE time I look up a designated AIP recipe, it includes eggs, nuts or something else that is NOT on the AIP list. I am so confused. I have avoided certain foods like the PLAGUE and then see “AIP” recipes that include the forbidden items. Just completely confused. Thanks.

    • Sounds like the recipes are Paleo ,that’s what comes after The AIP 30 day . Just reread the recipes ,a lot of them tell you what to leave out to make it AIP .

    • Dear Rachel, please look up Autoimmune AIP, or autimmune protocol. These recipes cut out eggs, dairy, nuts, seeds etc. I can’t tolerate any of the other stuff either, including fermented things and long cooked broths (histamine issues). Don’t give up. There are many of us.

  7. Hi Laura,

    I’ve had eczema for 40 years, but in the past 1 1/2 it has been the most severe it has ever been. After several doctors prescribed steroid creams again and again, I found a doctor that specializes in autoimmune diseases (I also have graves & alopecia). She asked me to try the Autoimmune Protocol. I’m 3 weeks in and although I feel good, my skin is still struggling to heal. I know it’s different for everyone, but how do I know if this is the right answer for me? Or could it be some food in the protocol that I should try to eliminate? Seafood, citrus? It’s not an easy task following the protocol, but worth it if the outcome is living without having to wear long sleeves everyday to cover the unsightly rashes all over my arms.

    • Hey! I just wanted to chime in, because I did the AIP for six months, and the first few weeks for me I started to feel better, but it wasn’t until I had been following it for about three months that I noticed that every single one of my symptoms was gone, and even then, I was having digestive issues which a year later I’m still trying to correct. I’ve read in forums that for some people it took a lot longer than it did me. I’m not a doctor or anything but I just wanted to chime in and say hang in there! 🙂

      • Thank you for responding! I just made it through week 6 and each week has been continuing improvement. I’m guessing for me it will be several months before I’m rash free for more than a couple days at a time. You mentioned you did it for 6 months. At anytime during the 6 months, did you add any food back into your diet?

        • hey!
          yes, I did add food back in. That was a whole process that was very frustrating, because I also have anxiety (which almost went completely away while I was on AIP) that made it so I couldn’t tell if I was having a reaction to the food, or having anxiety about having reaction to the food.
          I was successfully able to add back in some nuts and seeds and some dairy, and then eventually my doctor just did a food intolerance test on me and I gave up the AIP diet and just removed those foods. All my symptoms came back, so I’m planning on starting it again in a couple of weeks. 🙂

  8. Can I ask what the best options are I terms of carbohydrates for a toddler would be we generally eat starchey tubers sweet potatoes, white potatoes, etc. is yuca flour a good option? Also what are good alternate forms or calcium for a toddler if lactose sensitivity is present? Also wondering if there is a difference between Chris’ paler “code” and paleo “cure”? I have the former. Do they cover a lot of the same material? Thanks so much very informative article as always

  9. Hi! I am on week 2 of the AIP diet and suddenly have terrible heartburn! I’ve only suffered from heartburn previously during pregnancies, occasionally with bananas, and almost alway when I have an upper respiratory thing going on (post nasal drip related I believe). Why, oh why is eating AIP causing heartburn?!? History: diagnosed with “postpartum thyroiditis” 8yrs ago after first childbirth (I was VERY hyperthyroid for 3 months then crashed into hypothyroid. At the time, just followed the Drs advice and took synthroid. Wasn’t aware until later that my antibodies were though the roof and I was really suffering from Hashimotos). 5yrs ago during a period of stress (and after another pregnancy), became debilitatingly nauseous, couldn’t eat, stomach pains, lost a lot of weight. My amazing Chiro told me to take out gluten and ordered gluten sensitivity panels and those were also through the roof. At that time, I took out gluten permanently and dairy for 3 months. Over the last several years, I’ve felt OK most of the time on a gf, close to paleo diet (minus occasional GI pains that seem related to ovulation/mensturation and too-frequent gas) but wanted to try the AIP diet to see if it would help with my (self diagnosed)endometriosis and to see if it would help with the gi issues and maybe more energy (now on synthroid and cytomel) and to clear up the occasional brain fog that I can’t find a source to and just for the fact that I have autoimmune diseases myself and several in the family. Thank you!

    • Hi. Your symptoms sound just like mine. I have Hashimotos, Endometriosis and PCOS.

      I was curious how you are doing on the diet and if you have noticed any improvement?

    • I got heartburn very bad when I started AIP (I’ve been AIP for 18 months now). It wasn’t until I stated taking digestive enzymes with every meal that I finally got it to go away!

      • I have super similar issues as you, and followed aip for past year. Unfortunately one thing you dont hear about is how aip can create the deposits and i have gallbladder stones now-the heartburn /gallstone attack i had this morning, i literally thought i was having a heart attack (have svt and my mom had heart attack early in life). Anyhow, gallstones form from high fat foods and now i am stumped at what type of diet to be on. Basically listen to your body and if you start getting mote frequent heartburn or twinges after eating dont rule out gallbladder issues- below the right side of rib and my heart attack pain this morn i could also feel the heat up into my right ear. The nerve that connects to the gallbladder is there. I regret using bacon, salami so freely now and shouldve been more strict with 3 servings or vegies to one protein. Just something to be mindful.

    • Hi, I know this is a very late response and maybe not helpful. But I’ve experienced many of the same symptoms that you have and I figured out some of them which i think might help you. Or at least doesn’t hurt to try. So the acid reflux one, well after extensive research I learned that one of the possible causes is actually not having enough acid. So what I did that worked is I would drink a warm glass of water with 1-2 spoons of apple cider vinegar a half an hour before meals. It really worked and in the process I’ve also learned that it helps clear the stomach of toxins and inflammation. Now I would first suggest trying this at home and seeing how your body reacts to it because not to be gross but initially I had massive diarrhea but more of in the sense that it felt like a full colon cleanse. And I felt better after words. So don’t be scared by it. It will normalize. And so worth it. Also suggest drinking it with a straw because I learned recently that it can be corrosive to tooth enamel and again it works. Also I know for sure it’s getting rid of the toxins just by the fact that my adult cystic acne is even going away.

      Now for the brain fog, which bothered me the most and actually freaked me out. I discovered multiple things with this that you can try one at a time to see what really works for you since I don’t know exactly what was the true solution or if it really was all of the above. So one of the things I discovered along with my Hashimoto’s is that I’m vitamin D deficient. You would be surprised how common that has become now a days. Vitamin D is known to not only improve bones and help with joint pains, but it is also a mood elevator somehow. And i did feel a little clearer the more corrected it got. I also started taking fish oil tablets to reduce inflammation and it was found to really help with Hashimoto cases. Finally, I tried magnesium supplements. Now how I got to trying this is because I heard that sometimes vitamin d deficiencies could actually be due to magnesium deficiency because it aids in the absorption. After taking this I felt a lot better. I felt way more clearer. But the thing is that I’ve also started becoming more compliant with everything else around the same time. That’s why i say try and see what works for you. Another huge factor is having a consistent sleep and a morning schedule. I think it really matters for thyroid problems especially Hashimoto’s. I learned this because I’m also suffering from idiopathic hypersomnia, and saw a difference when I forced myself to wake up at 6/6:30 every morning and take my thyroxine right away as well as force myself to sleep early. It was definitely hard but i felt a huge difference and now my fatigue has cut down by A LOT and in general I feel better. Now I try not to let anyone interfere with my sleep schedule.

      Also of course cutting out things like eggs, dairy, refined sugars, fruits, processed foods, rice, and white bread helped. I discovered that I crash hard after those and/or get really bad brain fog. Now I haven’t gone full AIP diet, because its super hard especially breakfast. But I’m working on it! I actually came on here to see if anyone knows whether you can have lactaid milk on it or not. Do you happen to know by any chance? Oh and the whole menstrual cycle thing i get it. If you figured it out, please tell me! I noticed I also get a little word forgetful the closer to my period and I don’t know why. I’ve just been trying to record all my symptoms on this app called flo to see if any symptoms have correlation with my period and if so how can I fix it. Wow I wrote a lot. Well I hope this was helpful in any way for you or that you got it all figured out now. Good luck!

  10. Thanks for this article! I have Hashimoto’s and have been strictly gluten free for 2 1/2 months. I’ve also had absolutely no refined sugar and only minimal fruit. I have been so strict about this diet that I prepared every bite of food in my own home to avoid cross contamination. I have avoided possible cross contaminated foods entirely as well. I just had my labs done and there is no improvement in my antibodies and my TSH actually INCREASED! I was so frustrated until I came across your article and now I have hope that further restricting my diet may bring the change that I need. I do have a question though. I am naturally very thin (5’4″ 112lb. female) despite having an elevated TSH. After cutting out gluten and sugar, I dropped to 104lb which is definitely not a good thing. I have deliberately eaten more healthy fats to try to make up for my reduction in carbs, but apparently it didn’t have the same affect. I’m really afraid of losing more weight by restricting my diet even more…especially cutting out all grains as those are the biggest source of carbs for me. So how can a person like me implement the AIP diet or even just the regular Paleo diet without losing more weight?

    • Hi Katy, I just discovered the AIP approach a couple of days ago and am trying it myself but much like you I’m VERY concerned about my weight…I burn calories just thinking about it 🙂 I’m 5’1 100 pounds soaking wet! Did you get a response from anyone on your concern? I’d be so happy to hear any advice, I hope this fins you doing well and on the road to recovery. Thanks much. Warmly,


    • I lost 20 pounds on AIP (didnt want to). Now ive gained back almost all of it.

      The big culprit for me was going too low carb. Adding in a bit more cassava/plantains and a lot of fat (tallow, avocado, olive oil etc) helped. I also started eating 4-5 times a day.

      I guess when you eat cookies and stuff, its easy to maintain weight by eating 3 times a day cause you get snacks all the time. Up your meals, carbs and fat and most people on AIP should be fine.

    • I am in your same boat! 5’6” and 112 lbs. I’ve been gluten free and dairy free except for butter and occasional piece of far chocolate. I am dreading doing this diet because it seems no fun and actually stresses me out about it which isn’t good. I have hashimotos and alopecia and need to fix this hair loss. Just want to be guaranteed that I will get my hair back if I do the AIP diet!

  11. What do you suggest for person with Ankylosing Spondalitis, psoriasis, ocular uvitis, and gastroparesis?

  12. Hi Laura

    Great article – Can you say any more about what you would do with positive Array 10 markers? Would you still reintroduce these into the diet? After how long?

  13. Hi there! Man can I use some help. I recently read how gut issues can cause brain issues, as the two are closely linked. I’ve been negative, stressed out, and fearful for the past 20 years, which opened my gut/brain up to a slew of problems (including an inability to gain weight). The worst is this: When I eat the wrong thing, my head/brain becomes tangibly inflammed… it feels like a burning, tight band sensation all around my head; sometimes it’s mostly around my temples… It seems to move all over the place. It remains all day until I wake up the next day… and even then, they symptoms remain, though at a much lower level.
    I’ve held closely to a Paleo diet for a few years, but more recently the autoimmune Paleo diet (but probably not rigorously for a full 30 days). My problem is that it seems like EVERY single food I eat provokes my head symptoms… some less than others. So even though I’m on the strict paleo diet, I still struggle with the head symptoms. Is it possible that my gut is so compromised that my head will continue to react to all foods (at least until I’ve removed the most offensive foods for a full 30 days)? Or is it more likely that even though I’m eating the ‘right’ foods now, I will continue reacting to some degree until my gut heals?
    Like I said, I don’t think I’ve gone a full 30 days on the ‘strict’ diet. Eggs and nuts were usually in the mix somewhere… but now they’re out!!!
    Your advice would be greatly appreciated! I’m now adding mindfulness and meditation to the mix as well.

    • Hi Steve,
      That sounds so rough! As a Craniosacral therapist I’d say you may try to see an osteopath or Craniosacral therapist. It.’s interesting that it happens with every food you eat. It makes me think there could be an issue with a previous head injury that’s flaring. The worst that could happen if you go to a Cst or DO is that you’d feel relaxed and more clear headed.
      Best of luck!

    • Hi Steve, You are the first person ever that I have heard describe the exact same symptoms as myself. Every food, particularly any kind of starch, gets my head ‘buzzing’, or like pins and needles. Disrupts sleep etc. Did you ever find a solution? I’d love to hear your experience.

  14. Hi Chris,
    I’m wondering what your thought on the Swank diet is since you mentioned MS in this blog post. I looked at the study published in 1970 and it did seem like an anecdotal/correlational study, but the correlations were strong. I have the impression that the patients in the study didn’t experience full remission as did Dr. Wahls. But how do we reconcile this conflict? Could saturated fats cause MS?

    • I have MS also and I’m having a hard time reconciling the Paleo Diet with Swank. With all the restrictions there’s really nothing left to eat but leafy green vegetables.

    • Be careful with supplementing with iodine with Hashimoto’s. Absolutely ask a well informed doctor about this before you consider taking the supplement of iodine as an excess of iodine can cause lots of issues with the thyroid gland. Taking an iodine supplement wreaked havoc on my body and thyroid.

  15. Thanks for the comprehensive article Laura!

    You might like to have a look at the research of Dr George Jelenik (Australia) regarding multiple sclerosis. He is on the same page as you regarding lifestyle, stress management and whole foods diet however his research indicates eating meat should be avoided for people with MS, no matter how high quality. I personally know of many people who say their saw a great decrease in symptoms by following his recommendations.

    • I had ms i was a mess…. Then with diet i had a total recovery 100 percent and i forget of ms. I play rugby and have a totally normal life. I has a longgg history i did 1000 of therapies but paleo was the cure and drank bone broth too…. Litres a day

  16. I have had Hashimotos for over 18 years. I am 50 years old and have recently been diagnosed with a vitamin D difency and am in week 4 of a prescribed dose of D2 1.25mg (50,000 unit) once a week. I feel no difference on this medication, in fact worse.
    I have suffered with weight gain for the past 8 years or so, increasingly suffering from fatigue, headaches, sleeplessness, lack of concentration and so on which I read could be related to the vitamin D difenciey.
    I am not sure where to begin but I now I can’t go on like this.

    • Vitamin D2 is less effective with more side effects than D3. Get your doctor to tell you how much over the counter D3 to take and throw the D2 away.

      • I am about to complete my prescription and will go back in for labs.
        I will mention the D3 instead of D2. Things have leveled off but I am having muscle cramps in my calves from time to time.
        I read an article on magnesium – which is something that could need added to the D3/D2 deficiency.

      • Thank you Erin. I read the article – Epsom salt soaks, that is easy.

        shouldn’t my PCP track this or do I need a specialist and if so – what type

    • I too have Hashi. I highly recommend joining a group(s) on Facebook for help in this area as well.
      It is my understanding that it is Vitamin D3 that one should take to increase levels if one must supplement.
      Again, join Stop the thyroid madness (this one has a great website) or Hashimoto 411 as a suggestion. There are others as well

      • I was member of Hashimotos 411 FB and found it extremely helpful early on. I went Paleo first and the AIP and my antibodies dropped. and then I had to go back to regular eating for several months and they continued to drop. I am now in normal range and not strict paleo at all. Hashimotos 411 Facebook page would not let me post my story. They said it would confuse people. I said it would give them hope. They deleted my post and I was kicked off the site. Eating gluten is a no no to them and you can’t even mention that you do it. Ever.

        • Thats interesting. I wonder why they are against gluten although you succeeded to reintroduce it

  17. I was diagnosed with Ankylosing Spondylitis. I’m looking for a more natural approach to healing. First question do you know how to find a good holistic type dr in the Pittsburgh PA area? Second question… I’ve been thinking about trying the low carb or paleo diet but have some concern on how I could do that if I don’t eat meat. Do you have any suggestions?

    • Dr Jaison Golijuh…(I am fairly certain I have misspelled his last name) . Is in Butler/Renfrew area and Tracy Yautz is in Harmony. They are both naturopaths.

  18. I really love this approach to eating. A lot of people just can’t (and don’t want to!) maintain a strict diet and it’s great to see this kind of experimentation being recommended. If anyone is interested, I have a free worksheet over on my blog to help with planning and experimenting with this kind of eating (which I call ‘template eating’. Hope it helps! http://livethewhole.com/what-should-i-eat-template-eating/

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