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Getting To The Root Cause of Hashimoto's Thyroiditis

Hashimoto’s thyroiditis is an autoimmune disorder and the most common cause of hypothyroidism (an under production of thyroid hormone).

An autoimmune disease occurs when the body’s immune system mistakenly attacks its own tissues, seeing them as foreign. In the case of Hashimotos, the immune system attacks the thyroid gland, which regulates a broad array of vital body functions.

This thyroid disease, also known as chronic autoimmune thyroiditis and chronic lymphocytic thyroiditis, was discovered in 1912 by a Japanese surgeon named Hakaru Hashimoto.

Hashimoto’s thyroiditis typically causes a hypothyroid condition characterized by low or underactive thyroid function. It can affect both men and women of any age and can even occur in children and teenagers, however, it primarily affects women. The female-to-male ratio is at least 10:1. Most women are diagnosed between the ages of 30 and 50 even if symptoms presented long before that.

Which is why I wanted to write this blog.

Hormones are by no means my area of expertise, but I have happened to encounter Hashimotos and hypothyroidism a great deal within my coaching practice.

In this blog I’ll discuss the symptoms of hypothyroidism, the testing for it, potential causes, the differences in approach between conventional medicine versus foundational medicine and offer some suggestions for nutritional therapy and lifestyle intervention.

Hypothyroidism Symptoms

The thyroid is a small, butterfly-shaped gland situated in the front of your neck directly below your adam’s apple. The thyroid is a critical part of the endocrine system, which produces essential hormones in your body.

It literally influences the rate at which every cell, tissue, and organ in your body functions. This includes your bones, muscles, and skin, your brain, GI tract, and heart. Your thyroid does this through secreting hormones that manage how quickly and efficiently your cells convert nutrients into energy — otherwise known as your metabolism.

As Hashimoto’s progresses, it damages the thyroid gland, resulting in hypothyroidism. Hypothyroidism basically means there is an insufficiency of thyroid hormones being produced by the thyroid gland. In Hashimoto’s thyroiditis, the thyroid typically becomes enlarged and cannot make sufficient thyroid hormones. As your immune system continues to attack it, it gets bigger and bigger. Although it doesn’t hurt, you may find you have trouble swallowing or feel pressure. The condition can even cause what is known as a goiter in some individuals, and surgery may be necessary to remove it.

Hashimoto’s ultimately renders your thyroid nonfunctional. Eventually, it will do the reverse and shrink.

Without adequate thyroid hormones and a fully functioning thyroid, many bodily functions become sluggish, and as a result your health suffers.

Hypothyroidism can cause a range of symptoms related to a slowed metabolism, including:

Brittle nails

Thinning hair or hair loss

Intolerance to cold



Dry skin

Enlarged tongue

Fatigue, tiredness, sluggishness

Heavy or irregular menstrual periods

High cholesterol

Joint and muscle pain

Memory problems

Puffy face

Slowed heart rate

Trouble becoming pregnant

Unexplained weight gain

Hashimoto’s Thyroiditis Testing

Testing can help diagnose Hashimoto’s- although there are some pitfalls to be aware of.

For example many conventional doctors typically only check your TSH (thyroid-stimulating hormone) levels.

However, to fully understand your thyroid’s overall health and not miss Hashimoto’s or any other thyroid issue, you should request a complete panel if you suspect your thyroid function is suboptimal.

In addition to TSH, a full panel checks:

  • Antibody levels (TPO and Tg)

  • Free T3 (fT3)

  • Free T4 (fT4)

  • Reverse T3 (rT3)

  • Total T4 (thyroxine)

  • Total T3 (triiodothyronine)

Diagnosing Hashimoto’s can be challenging. It often takes time, often gets missed and unfortunately doesn’t happen until later in the disease process.

Common lab findings will show an elevated TSH and low levels of free T4 (fT4). Typically, this is accompanied by increased TPO (antithyroid peroxidase) and Tg (thyroglobulin) antibodies.

Here’s a few key points to consider when reviewing a full thyroid panel:

  • TSH is only a measure of hormone signaling from the pituitary to the thyroid gland. It tells it to make T4 but doesn’t give an indication of what the thyroid is actually doing.

  • The liver converts T4 to T3 (the active form of thyroid hormone). Lab results on these two numbers can indicate if the liver is contributing to thyroid issues. The bacteria in your gut also play a role in the conversion of T4 into T3. Stress in the GI tract, such as inflammation from dysbiosis, and leaky gut can impair this conversion process, and result in the production of an inactive form of T3 called “reverse T3” (rT3).

  • Too much rT3 can suppress thyroid function. When free T3 drops off and reverse T3 increases, it’s can be an indication that the body is under stress — GI issues, toxicity or even a pathogenic infection.

  • Toxins are the biggest causes of elevated thyroid antibodies. Infections are implicated, too.

  • When TPO and Tg antibodies are low, it’s reasonable to assume that autoimmune dysfunction is not a factor. Ideally, TPO should be less that 34 and Tg less than .9.

  • If the free T4 and T3 hormone markers are elevated, while total T4 and T3 markers are low, there's likely a testosterone dominance. If there are high total T4 and T3 markers and low free T4 and T3 markers, there's likely more of an estrogen dominance.

Also, keep in mind that lab results can fluctuate. In the early stages of the disease, people may actually show signs, symptoms, and test results indicating normal values or hyperthyroidism. This may happen because the destruction of thyroid cells is sporadic.

Potential Root Causes

Based on the research, autoimmune disorders are usually not attributed to one single causative factor, but rather the result of a combination of issues.

Infections, nutrient deficiencies, poor gut health, and toxin burden may all play a part in triggering autoimmune diseases.


Bacterial, parasitic, and viral infections are a primary reason for developing autoimmune conditions, including Hashimoto’s thyroiditis. Infectious pathogens are thought to play a significant role in autoimmune diseases. Specific pathogens can worsen autoimmune diseases as well.

In particular, the parasitical infection Blastocystis hominis and bacterial infection H. pylori have both been linked to Hashimoto’s disease.

Along with this, viral infections are often cited as a major factor in autoimmune thyroid diseases. For example, research has found a link between the Esptein-Barr virus and thyroid disease.

Other viruses or their components that have been found in the thyroid gland include enterovirus, herpes, HTLV-1, mumps virus, parvovirus, retroviruses, and rubella. Studies have yet to conclusively determine whether viral infection is responsible for thyroiditis but there is a clear relationship.

Nutrient Deficiencies

A healthy and nutrient-dense diet is essential for optimal thyroid function. Nutritional deficiencies that may be behind thyroid issues include:

B vitamins





Vitamin A

Vitamin D

Vitamin E


You can eat foods high in these nutrients to help support thyroid health. However, if your gut health is impaired and you are unable to properly metabolize and absorb these nutrients from food (or even supplements),you will still wind up deficient.

Which is why addressing the health of your gut can help positively impact the function of your thyroid.

Poor Gut Health

Compromised gut health and increased intestinal permeability (leaky gut) are involved in nearly all autoimmune conditions, including Hashimoto’s thyroiditis.

Chronic stress, food allergies/sensitivities, gut dysbiosis, infections, poor nutrition, and toxic exposure may all contribute to an increase in intestinal permeability.

This condition occurs when holes or gaps exist alongside the lining of your gastrointestinal tract. Issues, like the ones I just mentioned, can cause the spaces between cells to widen. This allows large particles — such as pathogens, toxins, and undigested food — to enter your bloodstream. Once circulating your body, the immune system mistakes these particles for foreign invaders and creates antibodies to fight them off.

This self-attacking immune response can result in autoimmunity and chronic inflammation.

The thyroid and the gut are inextricably linked via the gut-thyroid axis. The health and function of one impacts the health and function of the other.


Toxins are everywhere — in our air, food, households, personal care products, water, and more. They are unavoidable, but unfortunately can build up in our body.

This leads to inflammation and dysfunction of key bodily systems. Over time, an excess of toxins can contribute to or cause many ailments.

Biotoxins and environmental toxins are a leading contributor to autoimmune diseases and thyroid problems. They can damage proper immune balance, thyroid function, and overall wellness. These toxins include:


EMF exposure


Heavy metals

Lyme disease and other bacterial endotoxins

Mold mycotoxins

Parasite toxins and byproducts


Viral toxins

Conventional Medicine vs. Foundational Medicine Approach to Hashimotos

Conventional medicine looks to treat Hashimoto’s with thyroid medication that contains synthetic thyroid hormones — even for mild cases, such as during pregnancy.

The drug will likely be taken once daily and for the rest of your life. Some people also have surgery to remove the thyroid gland. Most conventional medicine practitioners view Hashimoto’s as a chronic, incurable condition. Basically, it’s an autoimmune disorder without any explanation of the root cause and how to address it.

The foundational and functional medicine world however, takes a different approach, looking to find the potential root causes of hypothyroidism symptoms. Foundational medicine also works to restore gut health and basic drainage and detox functions, which can in turn help areas like the thyroid.

Boost Iodine Intake

Iodine is a controversial topic when discussing Hashimoto’s. Some healthcare practitioners say iodine is essential for healing autoimmune thyroid conditions. Others say absolutely no iodine if you have autoimmune hypothyroidism.

For whole body wellness, iodine is essential. Every single cell in the body requires iodine.

So decreasing, minimizing, or refusing to take iodine because of autoimmune thyroiditis could harm many other areas of your body.

What’s the potential problem with taking iodine when you have hypothyroid issues? The supplemental iodine may bump up your TPO and Tg antibody numbers when they are already high (signaling autoimmune dysfunction).

Yet, you can still introduce the necessary iodine without raising the antibody levels. You just need to take it in much smaller doses and then work up.

To ease into it, try dosing with a broad spectrum mineral product and supporting your liver health for one to two months before adding an iodine supplement. This can help minimize an iodine-induced thyroid storm, plus increases in TPO and Tg antibodies.

Clear Infections

As I already mentioned, bacterial, parasitic, and viral infections are a main reason for developing autoimmune conditions. As a result, clearing these infections can help to heal an autoimmune issue like Hashimoto’s. A holistic, foundational approach can help to tackle infections. That approach includes taking supplements that support your drainage, detoxification, and immune functions. Some types of supplements that may help in your fight against opportunistic pathogens include:

Drainage supplements: Drainage pathways in the body do what I call “taking out the garbage.”

Having these pathways open and free-flowing is critical for healing from infections. Certain herbs and botanicals support toxin removal via your lymphatic system. Also, you should make sure you’re eliminating toxins regularly through your stools. This means addressing issues like conscription or slow moving bowels.

Detox supplements and binders: Your kidneys and liver process the bulk of toxins and send them out in your urine and stools. These organs benefit from extra support with herbs that support kidney and liver function. TUDCA, a water-soluble bile acid that can be taken as a supplement, also supports toxin elimination from your liver.

Parasite-fighting herbs: Parasites are a substantial drain on your immune system. Some also harbor the Lyme bacteria Borrelia and other pathogens. Taking parasite-fighting herbs may help you clear out parasite infections. Mimosa pudica seed also supports cleaning out parasites and other unwanted substances out of your gut.

Clear Toxins

Toxicity significantly contributes to health challenges, including Hashimoto’s thyroiditis. In many cases, the toxicity itself causes the deficiency.

Four common environmental toxins that mirror thyroid hormone structure and invade the thyroid gland are:

  • Heavy metals

  • Household toxins

  • Industrial chemicals and

  • Agricultural agents

Given the widespread presence of thyroid-damaging toxins in the environment, it’s important to strengthen the thyroid by avoiding environmental toxins as much as possible.

  • Transition to all-natural toiletries and beauty products free of heavy metals

  • Avoid using hand soaps and other cleaning agents with anti-bacterial properties

  • Limit your use of plastic containers for drinking and food storage or at least opt for BPA-free varieties (realize that they may still contain other bisphenol derivatives)

  • Invest in a quality water filter

  • Consume foods rich in iodine and selenium like seaweed, pastured dairy products, brazil nuts (organic) and fish (avoid farmed fish and opt for white or oily fish that have a short lifespan to avoid build-up of heavy metals like mercury)

  • Consume organic food as often as possible to avoid toxic agricultural agents

  • Replace non-stick cookware items with stainless steel or enameled cast iron options

  • Stop using pesticides, herbicides, and fungicides (or fertilizers that contain them) in the yard and garden

  • Make all living and working environments as serene as possible to reduce stress and support hormonal balance within the endocrine system

Heal the Gut

As I mentioned, the gut and the thyroid are inextricably linked. It’s important- if you suspect your thyroid is struggling- to address the health of your gut as well.

Some general guidelines for prioritizing the health of your gut include:

  • Avoiding antibiotics and unnecessary medications such as NSAIDS

  • Addressing slow moving bowels or constipation (the ideal is to eliminate 1-3x daily)

  • Consume natural fermented foods if tolerated

  • Address any underlying infections if present (TEST DO NOT GUESS)

  • Consume a balanced diet rich in plants and fiber

  • Reduce and manage stress

  • Avoiding the use of PPIS

  • Take an appropriate probiotic (link to probiotic blog)

  • Address the health and integrity of the intestinal lining.

Nutritional Therapy Strategies

Eating for the health of your thyroid isn’t as much about what you should not eat as it is about what you should.

In general, it can help to minimize foods high in soy protein, because large amounts of soy might interfere with the absorption of thyroid hormone.

It can also help to be aware of excessive iodine consumption, either in medications or supplements, as this could potentially alter your thyroid hormone level. Most iodine-rich foods, such as iodized products or fish, are fine.

But outside of these restrictions, it’s important to consume a rich and wide variety of foods you enjoy, that nourish your body, and that include lots of whole fruits, omega 3s, fiber rich vegetables, and lean protein.

While some practitioners will recommend a low carb diet for Hashimotos I tend to caution against it.

T3 is very sensitive to calorie and carb intake. If calories or carbs drop too low, two things happen: 1)T3 levels drop and 2) reverse T3 (rT3) levels increase (rT3 blocks the action of T3).

Some studies have shown that ketogenic diets in particular can reduce T3 levels, as much as 47% in just two weeks of a sub 50g carb a day diet. By contrast, people consuming the same calories but at least 50g carb a day saw no drop in T3.

I feel it’s important to prioritize the types of carbs consumed versus eliminating or restricting carbs altogether.

Some of the best foods to eat include:

  • Omega 3 fats like olives, olive oil and avocado

  • Plant based MCTs and saturated fats from coconut oil

  • Fermented foods if tolerated

  • Organic bone broths

  • Pasture-raised animal products

  • Sea vegetables

  • Wild-caught fish especially tuna. Tuna can be exceptionally beneficial for those with a thyroid disorder. Tuna is rich in selenium, iodine, and tyrosine, all nutrients needed for the production of thyroid hormones. Selenium helps convert T4 into T3, but it also protects the thyroid gland from free radical damage since it is an antioxidant mineral. The thyroid needs both tyrosine and iodine to produce thyroid hormones.

Include foods or herbs rich in:

  • Vitamin A — found in broccoli, carrots, spinach, and sweet potatoes (if oxalates are of a concern lightly steam or cook vegetables such as spinach which will all but eradicates oxalates.)

  • Vitamin D — found in cage free egg yolks, fish liver oils, mushrooms, and wild-caught fish

  • Vitamin E — found in almonds, avocados, and sunflower seeds

  • B vitamins — found in leafy greens, legumes, liver, meats, pastured eggs, and wild-caught salmon

  • Magnesium — found in green leafy vegetables, nuts, organic dairy, potatoes, quinoa, and whole wheat (Avoid if gluten is an issue. There is an association between celiac disease and Hashimoto's but the research is inconclusive. A gluten-free diet may benefit those with Hashimoto’s)

  • Omega-3s — found in fish liver oils, nuts, seeds, and wild-caught fish and seafoods

  • Selenium — found in Brazil nuts, organic dairy, pastured organ meats, some plants (if grown in soil with selenium), and wild-caught seafood

  • Zinc — found in pastured red meats, and some wild-caught seafood

You can also approach your dietary choices with a focus on fighting autoimmunity. In an autoimmune diet, you crowd out pro inflammatory foods by loading up on anti inflammatory foods instead. To limit inflammation, crowd out:

  • Fried foods

  • Margarine, lard, shortening, and trans-fatty acids

  • Processed meats and red meat

  • Refined carbohydrates

  • Soda and other sugary or high-fructose corn syrup beverages

And load up on anti inflammatory foods like:

  • Avocado, coconut, and olive oils

  • Green leafy vegetables

  • Low fructose fruits

  • Nuts, like almonds and walnuts

  • Wild-caught fatty fish like mackerel, salmon, sardines, and tuna

Final Thoughts

Hashimoto’s thyroiditis is a chronic autoimmune disease that causes an underactive thyroid and its associated symptoms.

As it’s the most common form of hypothyroidism, it should be the first checking point if you are experiencing thyroid challenges.

It’s crucial not to allow symptoms of thyroid issues, including Hashimoto’s disease, to go unchecked and unaddressed.

If you suspect a thyroid issue, make sure you get thorough testing for an accurate diagnosis and then work toward healing with a qualified professional.

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