Autoimmune Disease And The Autoimmune Protocol Diet: An Introductory Guide

Last updated on May 25th, 2019 at 1:50 am


[Last updated: 9th January, 2019]

Autoimmune diseases are more common than ever before.

The alarming increase in asthma, Crohn’s disease and type 1 diabetes in children are testament to that fact (1, 2).

Unfortunately, our scientific understanding and treatment protocols for autoimmune conditions have not progressed at the same rate.

The Autoimmune Protocol diet (AIP) has since emerged as an all-diet approach to treatment; one that is making its way into mainstream medicine.

This introductory guide looks at the pros and cons of the AIP diet and explores how it (potentially) works.

What Is The Autoimmune Protocol Diet (AIP)?

What Is The Autoimmune Protocol Diet (AIP)?The Autoimmune Protocol (AIP) is an elimination diet designed for those with an autoimmune disease.

It is a restrictive eating pattern said to have emerged from the Paleo movement (and sometimes referred to as Autoimmune Paleo as well as Autoimmune Disease Diet). But to describe it as Paleo seems too unscientific, and also a term I don’t like to use (for reasons outside the scope of this article).

On the surface AIP sounds like just another fad diet, but it’s simply an extremely nutrient-dense diet that excludes all known or suspected gut irritants. Emphasis is also placed on non-nutritional aspects of lifestyle known to influence symptoms of autoimmunity. This includes things like managing stress, prioritising sleep and regular exercise.

The Autoimmune Protocol is not a cure (autoimmune diseases are not reversible) but it can make you symptom-free, at least according to patient testimonial.

Summary: The AIP is an elimination diet designed to help treat all forms of autoimmune disease. It is not a cure, but a long-term holistic approach based around the removal of gut irritants from the diet.

How Does It Work… Is It A Universal Autoimmune Disease Diet?

An autoimmune disease is a condition that develops when your body’s immune system mistakenly attacks healthy substances and tissues in the body.

How does the autoimmune disease diet work?
Image source:

Over 80 other illnesses are caused by autoimmunity (such as Fibromyalgia, rheumatoid arthritis and hypothyroidism), but new research suggests they may all have the same root cause…

A combination of imbalances in gut bacteria (gut dysbiosis) and low-grade inflammation (inflammation in our cells) (3, 4).

The Autoimmune Protocol is said to help eliminate certain food chemicals and compounds that cause gut dysbiosis and low-grade inflammation in sensitive individuals. Cutting out these foods (in theory) reduces inflammation and gives your body the opportunity to recover and “reset”; known medically as remission.

This is what celiac disease patients experience when they go gluten-free, or most IBS patients when they follow a low FODMAP diet.

Once in a state of remission (symptom-free), you can then begin slowly reintroducing different foods. These so-called “food challenges” show you exactly what you can tolerate, and how much.

Based on this theory and process, the AIP is considered a “universal” autoimmune disease diet as it may help with the entire spectrum of autoimmunity issues.

Summary: It is thought all autoimmunity issues arise because of gut dysbiosis and low-grade inflammation of our cells. The AIP diet helps you to identify and eliminate foods that fuel these problems; at least theoretically.

Is There Scientific Evidence To Back This Up?

Is there any evidence to back up the AIP

I’ll admit I was highly sceptical of Autoimmune Protocol diet at first.

It remains theoretical (unproven) because researchers in the area of rheumatology/immunology rarely do randomised trials on elimination diets (the only way to prove “cause and effect”).

But that means it has not been disproven either. The proposed mechanisms behind this theory are founded on preliminary studies and it is certainly an intriguing area of nutrition science.

And it also means that overall, researchers still cannot reliably say what foods influence autoimmune diseases and their symptoms (nor to what extent).

Does the AIP help because:

  • You cut out specific trigger food components?
  • Such a restrictive diet inadvertently forces you to eat healthier on a consistent basis?
  • Or is it a combination of both?

It’s hard to say, especially when the majority of elimination studies have only looked at gluten. And even that area has heavily mixed results (5, 6, 7, 8).

There are so many aspects of health where basing decisions on non-trial and anecdotal evidence (personal testimonial) is dangerous and irresponsible. But when it comes to autoimmune diseases and the lack of nutrition research, it seems irresponsible not to.

Summary: The lack of clinical trials around autoimmune diseases in general – let alone on the influence of nutrition and elimination diets – leaves us without any solid recommendations. Theoretically AIP can help, and anecdotally it has a great track record.

What Foods Are Excluded?

What Foods Are Excluded on AIP?The Autoimmune Protocol is a strict elimination diet.

That means no food from the following categories may be consumed at any time, at least for the first 30 days:

  • All grains and pseudo-grains
  • All legumes, nuts and seeds
  • All nightshade vegetables (such as potatoes, tomatoes, peppers (capsicum), chilli and eggplants)
  • All forms of dairy
  • Eggs
  • All modern vegetable oils
  • All alcohol
  • All products with added sugar or sweeteners (both natural and artificial)
  • All food additives (such as emulsifier or thickeners).
  • NSAIDs (like ibuprofen and aspirin). Speak with your doctor first.

As you can see the Autoimmune Protocol requires some debatable exclusions.  Namely legumes, nuts, wholegrains, dairy and nightshades.

This means a lot of upfront meal preparation and a big shift from what the typical Western diet looks like. It also makes dining out with others very challenging.

What Foods Are Included?

What foods are included in the Autoimmune protocol diet?With so many foods cut out, there is an emphasis to eat more nutrient-dense foods including:

  • Vegetables of all kinds and colours (except nightshades). Especially cruciferous vegies like broccoli, cauliflower and cabbage.
  • Good quality seafood, particularly fatty fish rich in omega-3 fats.
  • Quality meats, especially organ cuts (offal) such as liver. Offal is some of the most nutrient-dense food we can eat.
  • Quality fats such as extra virgin olive oil, avocado, coconut oil (to a lesser extent).
  • Fermented foods (probiotic sources) such as kefir, pickled vegetables, sauerkraut, kimchi.
  • Fruit in small quantities.

Sample Meal Plan For The Autoimmune Protocol

This is a sample meal plan to give you an idea of what a day in the life of AIP looks like.

Meat will feature more often than not, and most meals and snacks require some advanced planning and prep:

Breakfast: Beef breakfast sausage

Lunch: Home-made tuna salad topped with extra virgin olive oil

Dinner: Beef steak with roasted vegetables

Snack: 1 banana

Drinks: Water or herbal tea

Who Should and Should NOT Try It?

Who Should and Should NOT Try AIP?The Autoimmune Protocol may be beneficial for anyone with a diagnosed autoimmune disease that has not been successful in managing their symptoms.

So those who have changed their lifestyle and eating habits significantly but have yet to notice any meaningful improvements to their symptoms.

The exception is type 1 diabetes, as this is related to pancreatic insufficiency. The only possible diet change that may help is a low-carb diet.

The reasons for those who should not try it are more extensive however, because of its restrictive nature. AIP may not be appropriate right now for those:

  • with numerous other diet-related medical conditions (always speak with your doctor first)
  • who are at risk of eating disorders, food aversion or emotionally fragile
  • with inflexible eating habits or unwilling to take on a dietary experiment right now
  • who do not have a diagnosed autoimmune disease.

It goes without saying that the autoimmune protocol is unnecessary if you do not have an autoimmune disease. There is no need to fear any food groups (including grains) if you are otherwise healthy.

Summary: AIP is for individuals who continually struggle to manage the symptoms of their autoimmune condition. But there are several important reasons why it may not be appropriate for certain individuals.

Recommended Resources

This article really only scratches the surface, and following the Autoimmune Protocol is a big commitment.

Although only temporary, elimination diets like AIP are highly restrictive and can get complicated if you take medications for other medical conditions or are at risk of nutrient deficiencies. It’s fundamental you speak with your doctor before beginning.

If you have an underactive thyroid I recommend you start with these dietary changes first and then re-assess.

Likewise, if food intolerance and digestive issues are your main concern, a low FODMAP diet may be more clinically relevant.

That said, for more information I recommend reading about it here and here. AIP is not guaranteed to work, but it reportedly has a solid success rate if you can stick to it properly.

About Joe Leech, Dietitian (MSc Nutrition & Dietetics)

Joe Leech is a university-qualified dietitian from Australia.

He graduated with a Bachelor's degree in exercise science, followed by a Master's degree in Nutrition and Dietetics in 2011.

Learn more about him on the About page

47 responses to “Autoimmune Disease And The Autoimmune Protocol Diet: An Introductory Guide”

  1. Thank you for your efforts to help me and other people like me.
    In my case I lost weight before getting RAI Treatment to blow away my thyroid something now I wish I did not do. My weight went from 105 kgs to 80 kgs then after RAI I went to 136 kgs and I could not stop the weight gain, I gave up soft drink, biscuits, lollies most junk food but still could not stop the weight gain, I have begged my Doctors for help but all they say is my thyroid levels because of medication are normal and I should be able to lose weight. BULLSHIT!!!! I would eat even this if I could lose weight, my energy levels have decreased , I fatigue easily, It is very hard to get motivated, I am going on a camping trip isolated for a month only taking healthy food in small amounts to see if I can lose any weight at all, as much exercise as I can tolerate but it is difficult when your body is carrying 36 kgs more than your set point. So any advice you can give me or sufferers of RAI Treatment may be able to pass on would be appreciated, and if I have any success in my venture to lose weight I will gladly pass on to you as we are all in the same boat. Cheers Bruce

    • Hey Bruce sorry to hear about your hard time.
      Look in your situation it’s definitely not just a matter of calories in calories out.
      Before you look into AIP, howcome you had RAI?
      Assuming you didn’t have an autoimmune disease then?

    • It’s been almost a year Bruce, how are you doing now? Have you found anything that works? I too had this issue. I have been fit most of my adult life with the exception of when I was pregnant. Even if I gained a few pounds I was always able to lose it just by adjusting my diet or adding some more activity. Then one day I started packing on the pounds and what used to work to lose the excess baggage, no longer did. My muscles were disappearing, I was tired all the time, I had no motivation and I couldn’t seem to stop eating. I felt hungry all the time.My brain and tongue didn’t seem to be on the same page My husband even threatened to put me in a nursing home, at the age of 40!. I was diagnosed with Hashimoto’s. I took high doses of Levothyroxin and then Armour. Nothing seemed to help with the weight loss. And no matter how much weight training I did, my muscles were non existent. I couldn’t understand this. So I decided to start drinking protein shakes. My stomach is sensitive to whey and soy so I began to drink vegan protein shakes. After about a week of having a shake in the morning and again at lunch time, I started to notice my muscles returning! I spend 20 minutes on the treadmill (fast walking) and then I weight train for about 40 minutes. I do this 3 to 5 days a week, depending on my activity level outside the gym. After about 6 weeks, I have lost 12 lbs and 19 inches so far and feel awesome. This is huge for me because I have had no success with weight loss in the past 5 years. I am no longer tired, my brain fog is gone, I can go 16 hours without eating without getting hungry! And I look pretty damn good too! I hope this helps you Bruce. I wish you luck because I know exactly how you feel!

    • I have hypothyroidism and i managed to lose weight two times since I was diagnosed! it is very hard to lose weight the only way I was able to do it was to try to heal my gut. I went to a naturopathic Doctor and he put me on 36 vitamin and mineral type supplements a day on top of that I was not allowed to eat any source of sugar not even from fruit for at least a month! no dairy no bread absolutely no sugar and I did manage to lose about 32 pounds. I was able to manage a pretty good diet for about six months then slowly I went back into my old habits. The diet and supplement regimen was hard and expensive but it is the only thing that has worked for me. I’ve tried different calorie intake’s Boot Camp classes you name it !!

  2. I never had a problem until one night at my daughters I was getting severe chest pain, I thought I was having a heart attack, the only relief I had was leaning against the wall with my arms above my head, like trying to push a wall over, this I had to do for most of the night everytime I laid down on the bed the chest pains would start again. I stopped eating much as I thought it was heartburn and I was sleeping sitting up in bed drinking heartburn medicine like a drunk at a free beer party, but no relief, coming home one day I got the severe chest pains again and was going past the Hospital so I went in I remember the pain eased and I was going to leave when the Doctors wanted to monitor me. My heart was racing at about 180 beats a minute so I can only guess at what rate my heart was beating when I had the pain, they blood tested me and found a thyroid problem, I was sent to a specialist who put me on about 10 tablets before suggesting RAI Treatment, I did not know the side effects so took the RAI Treatment willingly, now with this weight gain I wish I would of sought other options, carrying 30 kgs of weight around is not only damaging to your body but it eats your soul away when you look at Jabba the Hut in the mirror, depression, fatigue no libido are just a couple of reflections of your new life, you have become a big fat slob that no matter what you try, you just cant lose weight. Bruce

    • You thought you were having a heart attack yet opted to hold up the wall instead of going to urgent care.
      Research dry fasting and desperately, the keto diet. Alternate dry fasting with the diet. Start dry fasting slowly and work your way up. For example; Dry fast for 24 hours then eat keto for 2-3 days then dry fast for 48 hours, then eat keto for 3-4 days, etc. This will balance your hormones, cause you to loose inflammation, toxins and fat, and eventually get you healthier. Good luck.

  3. I have lupus and fibromyalgia with ever increasing pain. I have tried all the on-label meds. I’m running out of options. After hearing some testimonials from various, unrelated people about successful pain management through various diet restrictions, I decided why not try this one. Sounded healthy and like something doable, especially with a cookbook with meal plans. I stayed on it for four months. There was absolutely no change in my symptoms, nor was there a difference when I added all of it back in at once (which I did because I got fed up with all the restrictions that had no effect). My rheumatologist said from the start that few of his patients got any relief from any of he various autoimmune diets, but since they always seems healthy, he had no objection. On the up side…I did lose that 20 lbs. I’ve been wanting to get rid of!

    I so want something that works. I so do not want to waste a bunch of money trying junk. Any recommendations you may have for other things that have some sound science behind them would be welcome.

  4. And I was pretty rigid about it, which was super frustrating at times. major damper on social interactions. Only real break was when I had to travel for a week to a small town for a funeral. I tried to cook as much as I could without being antisocial. That was at about 6 weeks in.

  5. I agree completely with Stacie. I have fibromyalgia as well. I just did 4 months of the AIP diet and I was very strict. I didn’t put a foot wrong once. There was absolutely no improvement at all.

  6. Thanks so much Joe for this article. I have Celiac disease, hypothyroidism, eczema and hives. I have three sisters and we all suffer from Celiac disease but with different side effects. I eat well lots of vegetables etc but probably do over eat a bit. I rarely, rarely have takeout, I have never smoked, don’t drink alcohol anymore, have used olive oil when cooking for 30 years, have cut down on red meat to barely eating it at all, rarely eat lollies etc and yet my weight keeps climbing. My husband eats the same as me, enjoys his red wine and occasional beer, drinks coffee and is losing weight! I just don’t get it! I am in my early fifties. I have had a CT scan on my heart and it is clear of plaque, but my cholesterol is high. It has been since I was a teenager. I take medication for my hypothyroidism and stick to my gluten free diet. I have been on immunosuppressants, prednisone, antihistamines – you name it. I just don’t know where to turn next. So I would like to give the AIP diet a chance and maybe something good will come of it. Really enjoy reading your website articles – thanks again.

    • Hi Jenny thanks for the kind feedback 🙂 YEs in your situation it seems AIP is worth a try, because something is going on with your immune system and hormones that conventional medicine is not aware of yet. How’s your portions sizes, how many times do you eat per day?

    • Great informative article.

      I have been following Low FODMAP for over a year now with no improvement to gut motility (IBS-C). However I do not have the painful cramping any more, so it has still been worth it. I do have Ehlers-Danlos which is known to cause gastro intestinal issues so that may be part of why I still have problems.

      Currently I also have issues with fatigue, depression, weight gain and joint/muscle pain. I have recently been diagnosed with hidradenitits superitiva (I don’t recommend a Google image search – mine is at a much earlier stage than most of the photos online). HS is an autoimmune disease and is managed with long term antibiotics and horrible sounding skin graft surgeries. I hate the idea of putting medicine into my body which might cause more side effects so I was looking online and saw that people following AIP have had their HS go into remission.

      However I’m also Low FODMAP and have only just started to overcome an eating disorder (ARFID/SED), so I’m not sure that restricting my diet further is a good idea.

      On the other hand, I already limit grain intake and don’t eat dairy or pulses, so maybe the transition wouldn’t be that difficult. Except for potatoes, quinoa and rice…

      Would be grateful for any thoughts you may have.

      Jenny, sorry to hear that you haven’t found any relief yet. In relation to your hives, have you considered potential allergies? I was having hives quite a lot and eventually figured out that my allergies were caused by onions and garlic. Now that I completely avoid this family of foods I no longer have the allergy symptoms. Maybe try keeping a food diary and monitoring your symptoms.

  7. Hello, do you have any recommendations for someone who does not eat meat (vegan diet)? I’m not sure how long I could last on salads and veggies, but if rice and potatoes are definitely excluded, I can try. Thank you!

  8. I have an autoimmune disease called Wegner’s – it is a disease which attacks the blood vessels (Vasculitis) It usually attacks the kidneys but, in my case, it has just attacked the lungs. Also causes severe fatigue and gastric distress and aching muscles. I have always been on a very healthy diet, have now alos given up coffee, dairy (except for one pat of butter a day), and gluten. Eat very little sugar – only what is in a few foods. Do not eat any fast or prepared foods.
    Do you think this diet will help?

  9. Hi there, i am hypothyroidism and i have been struggling for the past 8 yrs. I did all different types of dieting and exercises. I do lose couple of pounds and inches but than after 4-5 days i wake up in one day and find my self fat as i used to be. And here we go again, it is very frustrating and stressful. Thats been like this for the past 8 years. I really need help because i am honestly loosing hope. There is nothing that i didnt try. I tried fastin diet pills, exercising, strict diet, herbs all different kind and i now i ran out of options. Help help help. I used to be 118 before my diagnosis and now i am 180 and counting. Thank you in an advance for any info thts given.


  10. This article and the AIP diet do address exclusions of some foods, but only because these foods may cause an allergic response. Ie they are the foods most commonly found to cause inflammation directly. But it does not address the metabolic controls or causes of nflammation. Increasingly, the literature cites insulin resistance, a high fructose intake and immune responses to wheat which include leaky gut syndrome, as causes of inflammation. In addition diatary restriction of fats also contributes to impaired metabolism.

    Many many people who have embarked on either a low carb, high fat or a ketogenic diet, have reported remission of autoimmune symptoms.

    Personally I have reversed my Type 2 diabetes and my fibromyalgia is in remission and my Hashimoto’s is stable. I am also losing weight.

    Looking at the suggested diet, I see a high carbohydrate intake, including the banana which is ctremely high in sugar and little or no fat. When you consider that the brain is over 60% fat and fat is the major component of healthy cell membranes , including the healthy sheaths of nerve cells, and hormones, you can see dietary fat xclusion can contribute to ill health. Both the LCHF and keto diets recommend inclusion of healthy animal fats rather than seed oils in the diet as animal fats have the most similar fatty acid composition to the fatty acids required by our bodies.

    If our tissues and nerves are repaired and replaced by our bodies than pain will persist. If we are allergic to a particular food and particles of this food enter our bloodstream because of a leaky gut, then inflammation will occur. This would heal if the body had access to the nutrients it required, including fatty acids. The porous gut is caused by Zonulin which results from an allergic response to gluten in the gut.

    Insulin resistance also causes an immune reaction as high levels of insulin círculate in the blood. Carbohydrate restriction lowers the insulin levels, so reducing inflammation.

    A high carbohydrate, low fat diet sets us up for immune reactions causing inflammations and a body unable to counter the inflammation and heal the site.

    The low carb, high fat diet in combination with restrictions of specific allergenic foods seems to produce the best control of inflammation. I’ve not seen anyone on a LCHF or keto diet report no change in symptoms, as reported here for the AIP dietg

    • The anecdotes you’ll come across depend on what sites you read. My symptoms got worse when I attempted a LCHF diet. Very low carbs can inhibit the conversion of T4 to T3. The sites I’ve read about it suggest 100-150g of carbs are minimum for good conversion rates. Although our bodies can produce glucose from glucogenesis, it’s not a very efficient process and may not produce enough glucose for optimal body functions, even though it provides for essential functions.

      People are different, and people change as they age. No one diet is best for all, we have to experiment and see what helps us individually. I’m trying the AIP now. I didn’t feel great on the strict protocol, so I started reintroducing foods quicker than I originally planned. Its been helpful though, because I’ve discovered nightshades cause inflammation, and I’ve confirmed that I need carbs but not much sugar.

  11. Sorry, I meant to say if cells and tissues, including nerve cells, are NOT repaired by our bodies ( having adequate nutrients including fatty acids) then pain will persist.

  12. I just heard about this diet, and I am really curious about it. I’ve been a type 1 diabetic for 4 years and I was just recently diagnosed with grave’s disease. I do not really have any symptoms (with the hyperthyroidism) for now, but I wonder if this diet would help me to maybe not get anymore autoimmune diseases. It is really strict though, I know I would have a really hard time. I’ll probably check with my dr and see what she thinks!

  13. I have an underactive Thyroid, most recent test showed my level right at 5. We have upped my Synthroid. I also have CREST Syndrome. Most recent platelet count was 519. Not sure of my SED Rate. I lost nearly 20 pounds following this restrictive diet almost 2 years ago. The holidays came and back on the weight came. Since then I can’t get the weight loss to restart. I battle with water retention like crazy. If it isn’t water retention it is acid reflux so bad it is insane. It is as if my body gets use to what ever I am doing and it laughs at me. I have most recently been on Profile by Sanford and initially lost 10 pounds and now you guessed it water retention. I have never been an over weight person until I quit smoking 5 years ago. Now I can not get this 30 pounds off and keep it off for the life of me.

  14. I am just in shock reading all these on autoimmune. Been suffering from this for 40 years plus. I have tried the diet prescribed unknowingly. What I did was to identify the food and what was causing all the allergic reactions. So I that and found out that only vegetables, fruits and proteins where okay with me.

    I did that for 3 years and half. I started eating proper food. Nothing happened for the first 4 months. By the fifth month I had strange and different reactions from the first types. Later, the first types of reactions started. A stranger one joined dizziness and falling asleep. I knew it was not sleep. More like passing out.

    Now, I want to go back to the diet that was fine with me only to find out that I can’t eat complete proteins. I will have terrible pains on the right side of upper abdomen. I pass out with the pain.

    Now I eat vegetables and some fruits.

    What should I do? In Nigeria where I am and come from this is our stable food and doctors think it is in my head. So much misery, I must say.

    • Maybe you should join the closed diet vs disease support group on Fb to see if someone else have same issue as you. Just search for ‘diet vs disease support’ group. Joe started the group. Also you can checkout posts from others and identify with their experience with food intolerance.

  15. I’am newly diagnosed with Hashimoto but have been sick with it for about 35 years they only tested me for Hashimoto because my Daughter has it I get pneumonia about every three months and in between Larngitits sorry my spelling is very bad and I have had fibromylia for 15 years at least I’am on disabilty so very tight budget makes it hard to eat healthy on a daily basis.The only way I have been able to lose weight at all was swimming assorted workouts for about 45 min then walking the mile in the pool.

  16. There was a controlled test of the AIP diet on hypothyroidism in 2016, full text available here: (scroll to the bottom of the article and you can find the PDF link to download the entire article with included images).
    From reading the article, the only people that got reduced TPO antibody counts were the ones that strictly followed removing the goitrogens.

    • Hey Stan the big issue with that study is that the treatment group did low carb high protein diet and no goitrogens, the control group did a regular high carb diet (not a low carb diet) and goitrogen foods if they wanted.
      So it is not just comparing goitrogens vs no goitrogens, it was also comparing low carb vs high carb, which means we don’t know which causes what.
      It would also have been nice if they swapped them around, so the first group did the other diet and vice versa.
      So definitely cannot make any conclusions from that study, especially as it goes against the weight of evidence.
      Would be great to test goitrogens in a clinical trial

      • Bottom of page 2941, beginning with:
        “Patients having anti-TG, anti-microsomal, and antiTPO Ab but who did not follow a restricted dietary regime (exclusion of the goitrogenic food mentioned above) showed a significant increase in autoantibody levels, in particular anti-TG Ab (+9%, P,0.017) and anti-microsomal Ab (+30%, P,0.028). Anti-TPO Abs showed a slight but not significant increase (+16%, P,0.004) (Figure 3).”
        From reading the paragraphs around that section, it sounds like they had several variations in the diet: some people followed the LCHF + no goitrogens, some only followed the LCHF part. That’s typical with any study: not everyone follows ALL of the plan as specified.

        In my case, I went from organic vegetarian to the LCHF part for the last 3 months with no changes in Synthroid for 5 months. I’ve been eating small amounts (5 to 20 oz) of both raw and cooked goitrogens the whole time along with the other veggies. I couldn’t get the Dr to retest the antibodies (I have Hashimoto’s), but the TSH dropped from 6.4 to 4.8 in those three months, with the free T4 holding steady at 1.1-1.2 on 25mcg Synthroid; the only change was the LCHF part of AIP. I’m eliminating the goitrogens for the next 6 months to see what that does. I’ve been following basically all of the AIP except for the goitrogens / cruciferous veggies, so now I’m going for the Full Monty. My TSH was running 9.5 without any Synthroid, and I had none of the classic hypothyroid symptoms except for a little sleepiness, and with Synthroid don’t feel any different. Dr wants to slam the Synthroid from 25mcg to 75mcg and I told her to forget it, I’d stay at 25. She doesn’t like being argued with.

        BTW, I’m purposely NOT trying for ketosis, and I monitor blood ketones (not piss strips) weekly to insure I don’t flip into it. Ketones are running 0.1 to 0.3 mmol/L. I’m nearly 60 and have Hashimoto’s; ketosis isn’t recommended due to my age OR Hashimoto’s from all I’ve read. Even with the age and Hashimoto’s, I have more energy than most people half my age. 😉 Diet is crucial if you want to live a healthy and long life. I’ve been skinny all my life, and now I’m even skinnier with the LCHF diet.

  17. Hello, I am hypothyroid (hashimoto’s with no antibodies). I gained around 88 pounds on l-thyroxine within a few years, no matter how healthy i eat and how much sports i did. I begged for combination therapy with T3 but was denied with lame excuses by incompetent doctors, though we know today that 20% of Hashimoto’s patients NEED extra T3, because they lack an iodase enzyme. (Read german article from Prof.Dr.Michael Derwahl, Berlin). He did a clinical trial on that topic. So I finally found a doctor who gave me extra T3 and finally I was able to get into ketosis again AND feel good on it (with T4 only i had massive side effects from ketosis like arrhythmias and muscle weekness so i had to stop eating ketogenic every single time I tried). Now I am eating a ketogenic paleo diet since 7 month and lost half the extra weight. I feel better on many levels with combination therapy, with T4 only I was literally a walking dead. So I recommend to use combination therapy (T4/T3) or maybe even NDT(natural desiccated thyroid) in combination with a low carb or very low carb diet (ketogenic). I am about to start the AIP protocol because I also have leaky gut with chronic diarrhea and that needs to be taken care of. Best wishes!

    • Can you provide the link to the T3 article by Prof. Dr.Michael Derwahl, Berlin, that you referenced in your comment above. i am having trouble locating it. Thanks.

  18. Hi Joe,
    How do I know which diet to try first? Low FODMAP, AIP or GAPS?
    I have multiple sclerosis, I’ve been gluten & dairy free since January 2014, I also went low carb for around 1.5 years and did well on that, lost 10kg/20lb.
    Things were going great, I gradually increased carb intake but still gluten & dairy free, it was fine for about a year then during last year I noticed I started to get a lot of bloating which has now become chronic. I get a lot of distention every night at bedtime, it flattens in the morning but no matter what I eat I bloat up through out the day till I look 5 months pregnant after dinner.
    I can’t figure out what the problem is so I’m going to get some pro-biotics and digestive enzyme tablets and try one of these diets, I’m just unsure which is best to start with, which would you recommend to start with? Thanks 🙂

  19. Hi Joe!
    I’m a 34 yr old woman with Graves’ disease. I was diagnosed last summer, i don’t have any kids but me and my husband were thinking on having kids my doctor recommended RAI to me because she mentioned getting pregnant under thyroid medication would take a long time and that if i continued with the pills I could even lose my “pregnancy window”. Ever since the RAI I gain close to 20 pounds. My levels are now “normal” and my doctor claims that i should be able to lose weight now. My energy levels are down, I’ve lost much hair, my joints hurt and lost my libido. I started having a protein shake in the mornings and clean don’t drink any sodas or processed food. Managed to go to gym 2-3 times a week (a win since I’m always fighting fatigue) and do weight lifting. I haven’t lost a pound (I’ve done this for 5 weeks now).
    I went to se a nutritionist (cost me $90) and she told me I was doing thinks ok. I started crying in her office when she aid I had to adjust to a new normal and that’s maybe I wasn’t going to lose the weight at all.

  20. Diagnosed with HLA-B27 uveitis in 1991. 2 years ago I stopped all gluten and the eye inflammation is gone. I was on a myriad of treatments to control the inflammation. The side effects were no fun, to say the least. Since I was told that HLA-B27 never burns itself out, I can only attribute my change to my gluten free diet. It is not as hard as it seems.

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