Hypothyroid Health Protocol


If you are hypothyroid, sorry to inform you, but you almost certainly have an autoimmune condition called “Hashimoto’s”. Having an autoimmune condition means that your body is attacking itself by antibodies from within. Having “Hashimoto’s” means that you have antibodies attacking your thyroid gland, in particular, weakening it to the point that it produces a low amount of thyroid hormone. Simply taking a thyroid hormone pill will not fix the autoimmune problem, it will only be like putting a band-aid on a deep, serious wound. Autoimmune conditions are caused by an underlying digestive problem – a problem called ‘leaky gut’, and triggers (i.e. such as certain foods) that go through your leaky gut into your blood stream and instigate antibodies to attack your body. Sorry to be the bearer of bad news. However, the first stage in addressing a problem is to be aware of the problem, and listed below is a regime to optimize your health and even reverse your Hashimoto’s autoimmune thyroiditis condition. If it seems like a lot to do at once, don’t worry, you can take your time and implement as much as possible at your own pace. However, the more you do, the better you will feel now and in the future. Personally, my approach was to do as much as possible at first – so I could jump start the healing process – and then ease up afterward. To each his own, but keep in mind at this point each day your body is being damaged more and more, damage that will take longer and longer to heal – or, at some point, will even be irreversible.  

Top 5 things to avoid: 

Avoidance is probably the most important step in order to get healthier. Why? Because it is not natural for the body to attack itself; you have been consuming unhealthy ‘triggers’ that have brought you to your current state of health. To reverse the condition, you need to avoid the triggers and give your body a chance to heal itself.

1) Gluten/Gliadin:

Gluten/Gliadin is found primarily in wheat, rye, and barley. Nowadays, most modern “wheat” products really aren’t even ‘wheat’ but a hybrid of it – even if it is labeled as ‘organic’ or ‘whole grain’. Hybrid wheat – in addition to the obvious culprits of bread and cereal – is often found in many processed foods such as sauces, snacks, and even processed meats. You’ll have to be careful to check the ingredients of foods if it does not say ‘gluten-free’. For many, gluten will cause digestive problems and an increase of thyroid antibodies – meaning each time you ingest gluten you are instigating antibodies to attack your thyroid. 

2) Dairy (especially cow dairy)

There has been a lot of hormone injecting, cattle cross-breeding, and gene splicing of the dairy cows making our milk products; the cow milk of today is not the same milk that our ancestors consumed hundreds of years ago – even if it is labeled as ‘organic’. Many get digestive problems from dairy, and it tends to elevate thyroid antibodies in many, as well. Some who switch to goat, camel and sheep dairy do not have issues, however. I try to stay away from it completely, but from time to time I do have goat and camel dairy, when available.

3) Soy

Almost all soy is GMO and wreaks havoc on the body, particularly the thyroid gland. However, even organic non-GMO soybean oil can lower thyroid production and cause problems with hormones etc. So, STAY AWAY FROM SOY. Some argue that edamame is ok, but I personally just stay away from soy period. Unfortunately, soy is found in a large percentage of processed foods – even ‘gluten-free and vegan ones’, so you’re going to need to check the ingredient list if there is no mention of ‘soy free’.

4) (Sodium) Fluoride

Fluoride is a natural occurring element that shows up in trace amounts in natural water sources; however, sodium fluoride, which is the additive form, is an unnatural chemical compound that used to be prescribed as a thyroid suppressor for those with overactive ones; in fact, it used to be nicknamed “The Thyroid Killer”. If you have hypothyroidism, you do not want to be consuming something that used to be named “The Thyroid Killer”. Unfortunately, sodium fluoride is found in tap water all across the world as well as in many brands of toothpaste, anti-depressant drugs, and in green and black tea.To go fluoride free you’ll either need to get a heavy-duty reverse osmosis filter – a typical Brita filter WILL NOT get rid of fluoride – or buy bottled water (that you make sure does not have added fluoride). A reverse osmosis filter for the kitchen sink costs around $300-500 dollars. You can get spring water delivered to your house on a bi-weekly basis for cheap – around $3-10 dollars every two weeks depending on the amount you order. Just google ‘water-delivery in ______ (enter your city)’. Make sure to order bottled water that has no fluoride added to it. 

5) Iodine:

Excessive Iodine intake has an incredibly high correlation with the development of Hashimoto’s autoimmune thyroiditis, and there was a study done where hypothyroid patients actually put their condition in remission only by cutting out iodine from their diet. Replace iodized salt with sea salt. I would go with just typical sea salt rather than pink salts because the latter tends to have high fluoride content (although the fluoride in pink salts is the natural form – not sodium fluoride – I prefer to avoid the controversial). Also, DO NOT supplement with iodine. Additionally, you might want to avoid seaweed, algae, and other ocean plants because they may contain high amounts of iodine as well. 

Top Supplements To Take (click the links to see recommended supplements)

The root of the problem of hypothyroidism is an unhealthy gut, not the thyroid itself. That’s why almost all hypothyroid sufferers are deficient in vitamins, minerals, and amino acids – because their bodies are not properly digesting/absorbing nutrients, which will make it more difficult for the body to heal itself. Generic multi-vitamins are usually full of synthetic versions (which can actually be more unhealthy than healthy), vitamins that cancel each other out in terms of absorption, incorrect ratios relative to one another, and additional ingredients that are on the ‘do not take supplement’ list i.e. iodine and immune boosting herbs. So here is a list of the supplements that you should purchase – note that all the ones that I have linked to go to the same website so that you can do the order from the same place all in one go:   

1) Take 30 mg of Zinc with 2 mg of Copper. Zinc and copper help boost thyroid production, especially T3 levels. They should be taken at a ration of 15mg:1mg (Zinc:Copper).

NOTE: Too much zinc will lower copper levels, and too much copper will lower zinc levels. Some have an imbalance of their zinc/copper ratio – i.e. someone who has already been supplementing too much with one of them or has used certain types of birth control that raise copper levels excessively high. In that case, you’ll need to adjust the ratio intake to create more of a balance between the two. Click here to read more on the subject. 

2) Take 200 mcg of Selenium with 400 IU of Vitamin E. Selenium is probably the most important supplement to take; it will lower your TSH AND antibody levels. NOTE: Make sure that the Vitamin E is soy-free (not derived from soy). 

3) Vitamin D – around 10,000 IU – most people with Hashimoto’s (and really in general) have a vitamin D deficiency. Vitamin D will help control the autoimmune condition, and it improves energy levels. 

4) Vitamin B complex (especially Vitamin B12) helps a lot with energy. Most with Hashimoto’s have B vitamin deficiencies, especially vitamin B-12. NOTE: Make sure that they are soy-free (not derived from soy). 

5) Ferritin supplement, which is similar to iron, but easier for your system to digest – yet still effective in raising iron levels. Iron boosts thyroid production and helps with thinning hair (for both men and women)

6) Probiotics to aid digestion and kill bad bacteria and yeast. NOTE: Make sure they are non-dairy.  

7) Collagen and Gelatin to help build the walls of the stomach and the intestines. NOTE: Make sure that they are soy-free (not derived from soy), though. 

8) Magnesium Oil Spray helps with sleeping and is a very safe way to supplement with magnesium (which most people, especially those with hypothyroidism, are deficient in). It also boosts your DHEA hormone naturally that improves your health in a lot of ways including your sex drive – which many people with Hashimoto’s have a problem with.  My DHEA hormone level was at its maximum level – without being excessively high – when I got a lab test after using magnesium oil spray. Do not supplement with DHEA hormone directly because if you supplement with any hormone external to the body, internally your body will stop producing it.

Note: Melatonin is also a hormone that you should not be taking because, once again, your body will stop producing it naturally. Shutting off the lights early and using magnesium oil spray is a better alternative to calm you down for a good night’s sleep. 

How to take the supplements: 

Almost as important as what you take is how and when you take them. Some vitamins will not get absorbed if taken with one another, or conversely, some vitamins will be much better absorbed when taken with other particular vitamins i.e. selenium will not be absorbed at all when taken in multi-vitamin form but is, in fact, better absorbed when taken with vitamin E, specifically. So, here is the order of the how and when you should take each of the supplements in your daily regime: 

Ideal Program:

Morning: 200 mcg Selenium with 400 IU Vitamin E (remember, SOY FREE) with breakfast. 

Lunch: B vitamins (soy free ones), Vitamin D 10,000 IU, Zinc 30 mg, and Copper 2 mg. 

Dinner: Ferritin and Magnesium Oil Spray at night before going to bed. 

Probiotics: Should be taken at the end of any or every meal. The more the better. 

Collagen and Gelatin: Can be taken whenever and as much as possible. 

Modified Program:

If the ideal program includes too many supplements, and you find it difficult to take supplements three times a day, follow this bare minimum one:

Morning: 200 mcg Selenium  with 400 IU Vitamin E (remember, SOY FREE) with breakfast. 

Night: B-Vitamins (well, at least vitamin B-12 and remember soy free), Vitamin D 10,000 IU, Zinc 30 mg, and Copper 2mg with dinner.

Probiotics: Include some form of probiotics in your daily diet in either supplement or food form. 

Top Supplements to NOT take:

When taking supplements, you are going to want to take what you know is beneficial for you and leave out all of the controversial. Below are listed supplements that, although recommended by some circles and found in many ‘hypothyroid’ supplements at health food stores, NEED to be avoided. You can click the links to get an explanation of why each one of these supplements is to be avoided. 

  • Iodine: Many say that supplementing with iodine is beneficial for those that have hypothyroidism; nothing can be further than the truth, however. DO NOT supplement with iodine
  • Immune Boosting Herbs: DO NOT take immune boosting supplements, for example: Echinacea, Ashwagandha, Licorice, Reishi Mushrooms, Spirulina, Chlorella etc. because they can ‘boost’ your immune system’s attack against your body and even direct it towards other parts of your body other than just the thyroid i.e. organs, intestines, joints etc. Even avoid ‘green smoothies’ if they include immune boosters such as spirulina and chlorella. 
  • Anti-Acids: Do not take anti-acids; most likely you have a problem of having too little stomach acid, NOT too much. Unfortunately, the symptoms of too much and too little stomach acid are about the same, causing confusion and serious health consequences if the wrong remedial action is taken. Note: in the link provided she recommends a stomach acid supplement; however, I suggest just mixing apple cider vinegar or lemon juice in a non-iced glass of water to drink before or during your meals that have meat in them (because meat can be difficult to digest for those with weaker stomachs i.e. most people with Hashimoto’s). 

Thyroid Hormone Replacement

It depends on what stage your thyroid destruction is at, but generally speaking, I advise not taking thyroid hormone replacement because anytime that you take an external hormone into your body, internally your body will stop producing it. Selenium, Vitamin E, Iron, Zinc, and Copper all will contribute to boosting your thyroid production, naturally. However, if you have been taking thyroid hormone replacement for a long time, you might need to slowly ween off of it and wait for your thyroid to heal itself – because you have been avoiding the top autoimmune triggers! – and begin to be able to produce its own hormone again. 

Dietary Guidelines: What to Eat

The ‘father of medicine’ Hippocrates stated, “All disease begins in the gut.” All autoimmune conditions start with the precursor of having what’s called a ‘leaky gut’; that is, your stomach and/or intestines become permeable and particles leave them into your bloodstream, which causes a defensive reaction by antibodies, inflammation, and damaged body tissue. To heal your autoimmune condition, you will need to heal your gut. Here are some general dietary guidelines to help with that: 

  • Eat Real Food: Meat, fruit, vegetables, nuts (though nuts can be difficult to digest for those with compromised digestive systems i.e. don’t go crazy with nut milks and almond flour although they’re better than dairy and gluten containing ones), rice (I’ve noticed that my body digests white better than brown), sweet potatoes/yams, and various kinds of beans (I especially like garbanzo beans). Try to avoid processed foods in general – i.e. baked goods, processed salt & sugar, candy, cereals, canned foods, and almost everything in a gas station, for example. However, when consuming processed foods get gluten, soy, and dairy free (AKA Vegan) ones. You want to balance your meals to include some kind of animal protein (eggs, meat, chicken, fish, liver etc.), a portion of carbs (beans, rice, potatoes), and vegetables (whichever kind of vegetable). 
  • Apple cider vinegar/Lemon Juice: Drink apple cider vinegar or lemon juice in water about 15 minutes before or during your meals that have meat in them – it helps aid digestion by boosting your stomach acid naturally – which you want! Many of those who think they are suffering from too much stomach acid, are in reality, suffering from too little stomach acid because the symptoms are nearly identical although the treatment should be completely different – you want to increase rather than decrease your stomach acid i.e. you should NOT be taking anti-acids. 
  • Fermented Foods: Before modern refrigeration, everyone fermented their vegetables so that they would last longer; now we don’t, and as consequence, we do not consume nearly enough probiotics in our diet. Try to include a lot of fermented foods in your diet to get probiotics. Remember, fermented foods should be dairy-free, though. Also, they shouldn’t be fermented with vinegar because vinegar kills the good bacteria. You can buy fermented vegetables at many grocery stores i.e. Kimchi and sauerkraut are popular and accessible options. Or, you can make it at your house by getting a jar, stuffing it with vegetables (any type of vegetables will do), pouring sea salted water in it, then closing it and putting it in a dark place (i.e. a cupboard) for 2-5 days. When you open it, it will be fermented and will have to be maintained in the refrigerator from that point onwards – so the good bacteria doesn’t die off. 
  • Anti-inflammatory Herbs (Food or Supplement Form): Some good anti-inflammatory herbs are ginger, cinnamon, turmeric, cumin, and Ginkgo Biloba. Try to include these herbs into your home cooking and make drinking these herbal teas part of your routine; you can drink the tea both hot and cold. Also, many of the sauces in Indian, Thai, and Nepalese food include a lot of anti-inflammatory spices, so find some good Asian restaurants around your area – although you have to stay away from naan and double check that the sauces don’t include any dairy when eating out at restaurants. You can take an herbal Ginko Biloba supplement along with meals. 
  • Simple Carbs & Sugar Intake: It’s good to have fruits, raw honey, and other sugary foods BUT you need to eat them on an empty stomach: when you wake up in the morning, at least 30 minutes before having a meal, and at least 3-5 hours after eating. Eating simple carbs on a full stomach, particularly after eating meat, will cause problems with digestion because simple carbs are meant to be digested quickly; if you eat them on a full stomach, they will take a lot longer to digest and unwanted stomach guests such as bacteria, yeast, and parasites will feed on it. Typically, people have an empty stomach after working out and simple carbs are an excellent post-workout snack because your muscles are craving them. I usually get my fruit and/or honey intake for the day early in the morning and just after working out. 
  • Soups: Traditional Chinese medicine considers soups to be the ultimate food for health and digestion because they are already ‘pre-digested’; that is, they are already warm and mushy so your digestive system does not have work to make them that way. HOWEVER, you must eat soups that are made with NATURAL BONE BROTH and NOT ones from cans, which have tons of unhealthy additives. So if you go to a restaurant you should ask them if it’s made with a homemade broth or if it’s from a can. If it’s from a can, DO NOT order it. Otherwise, make your own soups at home with homemade bone broth or with pre-made bone broth from a whole foods type of store. Bone broth is an amazing healer: it supplies the body with the gelatin and collagen it needs to heal. 
  • Limit Cold Beverages With Food: Your stomach is like a fire under a cauldron that heats up and breaks down the food you eat; drinking cold beverages will essentially put out your digestive fire and make it more difficult for your stomach to digest foods. Avoid iced and overly cold drinks during and after your meals. Also, you can ‘chew’ your cold beverages by leaving the liquid in your mouth for a moment to warm it up before swallowing. 
  • Aloe Vera: Just how aloe vera can heal your body tissue on the outside, it can also do the same on the inside i.e. leaky gut. You can buy aloe vera juice or the whole aloe vera plant at health stores and Mexican markets, for example. I prefer the whole aloe vera plant; I typically eat it by itself or blend it in a juice smoothie. 
  • Healthy Fats: Include a lot of healthy fats into your diet from sources such as avocados, coconut oil, and olive oil. Not only do I cook with coconut and olive oil, but I also use them as a moisturizer and even as a kind of hair gel. I pour olive oil over my food in place of using butter. 
  • Limit Caffeine: Caffeine can lead to blood sugar issues, diabetes, adrenal fatigue, and yes, leaky gut due to the release of cortisol – the ‘stress hormone’ – into the body. Furthermore, caffeine is not good for gut health hence that queasy feeling and loss of appetite that you get each time you consume it. This means to limit (I, too, enjoy some caffeine from time to time) coffee, tea (which you shouldn’t be having anyway because of its high fluoride content), yerba mate, and dark chocolate/cacao. Personally, if I do have caffeine, it’s usually yerba mate or dark chocolate because they do not contain fluoride and heavy metal pollution like tea does and coffee seems to upset my stomach the most out of all the available options. However, whichever way you consume caffeine, you must limit it because of the damaging effects of releasing excessive cortisol into the body. I would say shoot for once or twice a week max. Maybe start by limiting it to a small amount every other day. 
  • Cleanse: A body cleanse that includes cleansing yeast/candida, bad bacteria, parasites, and heavy metals will jump start the healing process a great deal. A large percentage of the world’s population in general – and those that have Hashimoto’s in particular – have an overabundance of yeast, bad bacteria, parasites, and heavy metals in their system (particularly lead, mercury, and aluminum). There is a large amount of crossover between the different cleanses i.e. the same herbs that kill parasites also kill bad bacteria and yeast. Also, the different issues are interrelated i.e. having high heavy metal content in your body will cause a yeast issue and having a yeast issue will make it difficult to kill parasites etc. Cleanses can be complicated; however, I generally just follow a healthy diet regime with a low amount of simple carbs & sugar – especially no eating simple carbs & sugars on a full stomach – along with taking cleansing herbal pills in the morning and at night for about 2 weeks. I usually drink a lot of juices, water, and do something to sweat a lot – i.e. saunas, hot yoga etc – during the cleansing period. I notice that I have to do a cleanse somewhat regularly (maybe 2-3 times a year). You will see a noticeable difference after doing a cleanse i.e. my skin becomes really smooth and vibrant. 

Written By: Eric Dunn

About the Author

I was diagnosed with hypothyroidism in January of 2014. After being diagnosed, I started to intensively research anything and everything that had to do with the condition. I found out that those with hypothyroidism, in fact, suffer from an autoimmune condition and not simply an underactive thyroid gland. This revelation pushed me to investigate what was the underlying cause of my health problem and how to solve it. After vigorous hours of studying, lab testing, and meeting with different medical doctors; I made a protocol that has since worked for me well: I initially tested at a TSH level of above 5 and a TgAb antibody level of above 500; however, after applying my diet and supplement regime I got my TSH to be below 2.5 – without ever taking any hormone replacement drugs – and my TgAb antibodies to 8 (which is within range) and my TPO antibodies to zero. If you have any questions and/or comments please leave them below, and I would love to try and help.

Though it might sound corny, cheesy, or cliche; when I discovered that I had an autoimmune condition I prayed to God to help me, and I told Him if He were to help me, I would try my best to help others. This blog post is me trying to do just that. I hope it does 🙂 .

Special Thanks

I’d like to give special thanks to a brave woman who suffered from passing out in public and warnings from doctors that she would never be able to have children. Crystal chronicled her journey to recovery from Hashimoto’s in her blog: ‘Hope for Hashimoto’s Disease‘, which helped me so much in my own recovery. She details how she went from having a high TSH and an exuberant amount of antibodies to having nearly a PERFECT TSH level and ZERO antibodies all without taking any thyroid hormone replacement. Furthermore, she ended up having a successful pregnancy and a healthy child. Much of what I’ve listed in this blog has come directly from hers. 

1 Comment

  1. Annie

    Hi Eric,
    Just wanted to say this was a great and very informative read. I really like the structured outline of supplements, as I’ve been currently trying to optimize a regimin. I have not gotten the official diagnosis of hypothyroidism (planning to see an endocrinologist soon) but I am always looking for homeopathic approaches to better health. You may know this already, but I’ve learned that vitamin D needs to be taken with a source of vitamin K to maximize absorption. Also, low doses of iron has more absorption power than high doses with much less side effects. I’m in the science field, so I try to sneak in some of my own research. In fact, right now I’m testing out an iron-infused spring water, called Spatone, which I like so far. Anyways, thanks for writing this and posting a link to Crystal’s story!

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