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Hashimoto’s Thyroiditis

Also known as autoimmune thyroiditis, Hashimoto’s thyroiditis is one of the top causes of hypothyroidism in America and it is becoming more and more prevalent. Thyroid disorders affect women more than men and it is often missed. Extreme fatigue is one of the primary symptoms experienced. By the time Hashimoto’s is noticed, if at all, the damage has often been done. Thankfully more and more doctors are screening for it. In this article, I will break it down, what is causing it, and what to do about it. For other thyroid disorders check out my previous article.


Your thyroid is a butterfly shaped gland that sits in your neck and is crucial in regulating your metabolism through your T3 and T4 hormones. Your metabolism is your ability to convert nutrients into energy. These hormones balance our energy and when they are off a variety of symptoms can ensue. Most commonly people suffer from hypothyroidism which is characterized by fatigue, weight gain, brain fog, and other symptoms. Hyperthyroidism is characterized by anxiousness, sleep disturbance, weight loss, and goiters. This by no means is an exhaustive list. And there are many causes to thyroid dysfunction. Our attention is focused on Hashimoto’s thyroiditis.

Hashimoto’s Thyroiditis

Hashimoto’s thyroiditis is an autoimmune disease of the thyroid gland. If you would like a more in depth view about autoimmunity check out my article on leaky gut. Otherwise, let me sum it up. About 80% of our immune system lies within our gut to evaluate what we are ingesting. Our gut is a primary way for pathogens and toxins to enter our body. I like to imagine our gut as a castle with a moat around it. We have several protective layers. Stomach acid is a major one. Human stomach acid has one of the lowest pHs in the animal kingdom. It is designed to kill pathogens as well as digest protein. Next is the castle wall or our cell wall. It is very selective in what it lets in or out. There is a moat in front of the wall too, a mucus membrane created by specialized cells which serves as another protective barrier. We also have trillions of bacteria, more than the summation of our own cells. They protect us and provide other benefits. Lastly, we have our soldiers, the immune system. These hone in on and screen everything going on in the gut. It is truly a remarkable system!

However, this barrier can get broken down. Through things we are exposed to, toxins we ingest, foods, and pathogens our intestinal barrier can become increased in its permeability or leaky. Leaky gut is a common issue these days and is problematic on many levels. Our immune system becomes activated creating localized inflammation to address the issue. This would be great if it was a one time occurrence. However, our modern lifestyle perpetuates the issues driving more and more inflammation. As the inflammation continues the immune system targets certain “foreign invaders” in its effort to clamp down on the problem. The invaders can be pathogens but they can also be foods. And in the case of autoimmunity, it is often foods. As it attacks these invaders, the inflammation can turn systemic. The immune system is on high alert because the issue is ongoing and chronic. This leads to the development of molecular mimicry.

Molecular Mimicry

Molecular mimicry is where the immune system broadens its search for the particular invader and starts looking for similar proteins. As it discovers proteins that are similar to the initial culprit, it targets them for destruction. We like to think that the immune system is out of control. Couldn’t be further from the truth. It is just on high alert because we are continually doing something that is harming us. The immune system is responding appropriately even though the consequences are quite damaging.

In the case of Hashimoto’s thyroiditis, certain proteins within your thyroid gland happen to look like the invader, the antigen that caused the initial inflammation. The immune system will target these proteins and begin the destruction of your thyroid, typically we are looking at thyroglobulin and thyroid peroxidase enzyme. When this begins often there are no major symptoms. But overtime they begin to arise.

How it Progresses

Hashimoto’s often goes unnoticed for a long time but a symptoms develop it may look like a rollercoaster. Often people drift between hyper- and hypothyroidism. They can have moments of high and then low. As it fluctuates more and more of the thyroid succumbs to destruction. At some point, hypothyroidism sets in with all its accompanying symptoms. By this point most people have been prescribed thyroid medication. The thyroid is essentially not keeping up with its tasks or is completely destroyed.

Once it is destroyed or not functioning at all, medication is required for life or some level of replacement. We must have thyroid hormones to stay alive. It is a vital gland. Thankfully there are many options, but our goal is to uncover the underlying cause and find natural support for the thyroid and immune system. And if we screen appropriately, we can even catch the process early sparing the thyroid.

Natural Approach

The first step is diet. I spend most of my time as a doctor addressing diet. I am sure it gets old for my patients. But I cannot stress it enough. Our lifestyles are so averse to our biology. We live in air controlled environments. Move so little that we need to supplement with exercise. And we work long hours and use artificial light so we can burn the candle at both ends. Everything we do is working against us. We try to supplement around our diet, but it is failing. Hashimoto’s isn’t the only one increasing, all chronic diseases are increasing at an exponential pace. No longer can we supplement around it and sweep it under the rug, as if we could do that to begin with. So our lifestyles need to be addressed.

I will summarize each one. And as blunt as I can sound I know this takes time. I know its hard. That is why I do what I do. I want to encourage others to be the best they can be. There is so much to be had when our health is optimal. We can enjoy time with our kids, our family. Go on vacation. See the world. Hike, backpack, and camp. The world is ours to enjoy.


selective focus photography of beef steak with sauce

Diet is top priority with Hashimoto’s thyroiditis. Nine out of ten times it comes down to a single food or two. Gluten by far is the most common. Remember molecular mimicry? Gluten can cause this. Just so happens that gluten looks like the protein in your thyroid. So many Hashimoto’s patients feel much better after they remove gluten from their diet. But gluten is not the only food intolerance. Other common ones are soy, corn, dairy, and nightshades. It is important to figure this out otherwise the inflammation will continue its vicious cycle.

Removing all inflammatory foods is also helpful. We eat a lot of processed foods and others that cause inflammation. So removing grains, processed foods, sugars, and pretty much anything boxed or packaged is important. Replace these foods with whole foods like high quality protein from pasture-raised, organic sources, organic fruit, and organic vegetables. For those who can tolerate dairy, I find it to be a great and healthy addition to any diet. Just look for antibiotic and hormone free, organic dairy. It is best if it is raw, but not always easy to find. Check for a local farmer near you.

A further note on protein. Our ancestors consumed a lot of protein. They also ate nose to tail. They ate the whole animal. It is very important to include organs in your diet. If you need a good company check out Heart & Soil, they sell organ supplements. Otherwise look for a local farmer. Another good website is, you can find local farmers there as well. Bone broth is another great food, so look into adding that into your diet. Check the ingredients though unless you are making it yourself. As for the amount of protein, aim for 1 gram per lb ideal body weight, in other words if you weigh 150 lbs eat 150 grams of protein. 100 grams of protein is roughly equivalent to 1 lb of meat. This will provide enough protein for all your daily needs of maintenance and repair. Crucial when trying to heal and support the body during autoimmunity. I will have an article out soon that goes deeper into this.

Herbs and Supplements

Inflammation is high with autoimmunity. Removing the culprit will help a great deal, but herbs can help a lot too. A lot of people suffer from multiple issues at the same time. Dysbiosis being a common one. Dysbiosis is an imbalance in the gut microbiome, all our bacteria friends. Sometimes we can have a pathogen causing issues or fungal overgrowth. Whatever it is, herbs are great at helping the body deal with it. So look into getting evaluated and what herbs may help you. Some of my favorites are neem and noni, Supreme Nutrition is my favorite company when it comes to herbs. But don’t take that as advice, getting evaluated by a competent functional medicine doctor is highly recommended.

Some herbs are really good at balancing the immune response which can drastically reduce the inflammation going on. But remember inflammation is a good guy, chronic is not. The goal is to not need to be on herbs all the time. That is why addressing the root cause is imperative. That being said, herbs are great at removing toxins too. They are crucial part of my approach.

Every now and then I need to give out supplements. Vitamins A and D are among the most common. They help regulate the immune system among many other things. Certain B vitamins may be needed, as well as minerals, but every patient gets evaluated for their particular needs. It is hard to know what is needed so I don’t really have a precise protocol that fits everyone. No cookie cutter approach, sorry! It would be nice though!

Stress Reduction

silhouette of man sitting on grass field at daytime

Lastly, stress reduction. We live high strung lives. We need to take a breather. It is very common for patients come to me with health issues and their lifestyle is contributing largely to it. They are often overworked. Maybe they are lonely. They might even hate their job. Some are having a hard time in their relationships with loved ones. Others are constantly thinking of the next to-do item. They never have a moment of rest. Literally burning the candle at both ends. Your body can take this for awhile but sooner or later the bill comes due.

It is important to evaluate priorities and reduce stress where possible. Sometimes it requires a career change. Sometimes it requires a relationship change. Maybe therapy. But things need to change. Some major ones I encourage are meditation and nature walking. I will throw exercise in here too, though it is quite difficult with Hashimoto’s thyroiditis and must be to tolerance or not at all in the beginning. Though I still encourage walking and other forms of movement. Nevertheless, exercise is a big component of a healthy lifestyle especially resistance training.

Meditation is like anything else it takes practice. Find a quiet place where there are no distractions. Sit comfortably and close your eyes. Focus your attention on your breathing. In and out. In and out. Whatever thoughts come, let them go. Try this for 5 minutes. Then 10 minutes. 20 minutes. Use calming music if it helps. There are many helpful apps and tools for it. But it takes practice. It is difficult to still your mind. But I promise it is so helpful and you will see the effect drift into the rest of your day. Take the mindfulness quiz and see where you are at! There are some helpful tools on that website as well.

Nature walking is very important. We are nature deficient. I often ask my patients to do this. Getting out in nature can help our immune system and improve our mood. Try it. Go for a walk in the woods. It is very calming.

These are some of the most important aspects in supporting the body and decreasing inflammation with Hashimoto’s. There are other aspects too. It wasn’t my intent to give an exhaustive list. But I hope this helps. So what’s next? You need to know for sure what is going on with the thyroid and that requires proper testing.


shallow focus photography of microscope

Most conventional doctors run only a couple of markers, TSH and T4. But it is imperative that you get a full thyroid panel ran. In functional medicine, our philosophy is to look for the root cause and one of the primary ways we do this with thyroid disorders is ordering a full panel. A full panel not only includes TSH and T4, but many other markers. We look at both the free and total versions of T3 and T4 hormones. We look at T3 uptake, reverse T3, and Free Thyroxine Index as well. All these help with determining the state of the thyroid and what type of thyroid disorder we are dealing with. But quite possibly and maybe more importantly we look at the antibodies to the thyroid specifically thyroid peroxidase antibodies and thyroglobulin antibodies. It is these last two that help us determine if it is Hashimoto’s thyroiditis. As for Grave’s disease another marker will be needed, just in case you wanted to know.

Once we get a full panel, the results will tell us quite a bit. I have had several clients who have come in with only TSH and T4 only to find out they had Hashimoto’s thyroiditis. Others have come in with only one of the antibodies ran and it was normal. Then we run the other antibody only to find out it is high. So it is very important to have a thorough examination.

As you can see it is not enough to run a couple of markers, but with functional medicine we need to understand truly what is going on. I often include these in my initial blood work with patients. But that depends on the patient. There other important markers we look at for overall health too. I think it is important if you are struggling with what could be a thyroid issue that you get it checked out. Maybe your GP will run these, or your chiropractor, naturopath, or functional medicine doctor. Either way, its best to talk to someone who understands all this so you can get this figured out.


I hope this helps. There is a lot I can go over. We are just scratching the surface on thyroid issues even just with Hashimoto’s thyroiditis. There are some great resources out there too. There is a good book by Dr. Datis Kharrazian on thyroid for those who want to learn more. Of course, I have other articles too on various topics including thyroid and you can always reach out to me, I would be happy to help or point you in the right direction.

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