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Hashimoto’s Thyroiditis: Finding and Addressing the Root Cause

Hashimoto’s thyroiditis is the most common cause of hypothyroidism in those over six years old. A Japanese surgeon, Hakaru Hashimoto, discovered the disease in 1912. (1)  

This thyroid disease is also known as chronic autoimmune thyroiditis and chronic lymphocytic thyroiditis. An autoimmune disease occurs when the body’s immune system attacks its own tissues, mistakenly seeing them as foreign. 

Hashimoto’s can affect men and women of any age and 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. (1, 2)

Hypothyroidism and Symptoms

The thyroid is a small, butterfly-shaped gland situated in the front of your neck directly below your Adam’s apple. The thyroid gland is a critical part of the endocrine system, which produces essential hormones in your body. (3)

Your thyroid regulates an array of key body functions. It influences the rate at which every cell, tissue, and organ in your body functions. This includes your bones, muscles, and skin to 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 — an activity you may know as metabolism. (4)

As Hashimoto’s progresses, it damages the thyroid gland, resulting in hypothyroidism. In hypothyroidism, the gland does not produce enough thyroid hormones to meet your body’s needs.

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 might have trouble swallowing or feel pressure. The condition can cause a goiter in some people. Surgical intervention may be necessary to remove it. (5)

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 your health suffers. (5)

Hypothyroidism can cause a range of symptoms related to a slowed metabolism, including: (4, 6)

symptoms Hashimoto's

Hashimoto’s Thyroiditis Testing

Testing can help diagnose Hashimoto’s. 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. In addition to TSH, a full panel checks: (7

  • 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 and doesn’t happen until later in the disease process. Common laboratory findings 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. 
  • When free T3 drops off and reverse T3 increases, it’s an indication that the body is under stress — most likely from toxicity and 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 than 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. (8)

Potential Causes

Based on research, autoimmune disorders are likely a combination of issues. Infections, nutrient deficiencies, poor gut health, and toxin burden may all play parts in triggering autoimmune diseases. Let’s take a closer look at these possible triggers.

possible sources of thyroid dsyfunction


Bacterial and parasitic 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. (9)

In particular, the parasitical infection Blastocystis hominis and bacterial infection H. pylori have both been linked to Hashimoto’s disease. (10, 11)

Along with this, infections are often cited as a major factor in autoimmune thyroid diseases. Research has found a link between Epstein-Barr (EBV) and thyroid disease. Other pathogens or their components have been found in the thyroid gland, including herpes, HTLV-1, mumps, and rubella. Studies have yet to conclusively determine whether a pathogenic infection is responsible for thyroiditis. (12, 13, 14, 15)

Nutrient Deficiencies

A healthy and nutrient-dense diet is essential for optimal thyroid function. Nutritional deficiencies that may be behind thyroid issues include: (16, 17)

  • B vitamins
  • Magnesium
  • Protein
  • Selenium
  • Vitamin A
  • Vitamin D 
  • Vitamin E
  • Zinc

You can eat foods high in these nutrients to help support thyroid health. However, if you cannot get the quality and quantity of nutrients you need from food, dietary aids are an option.

Poor Gut Health

Compromised gut health and 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 lead to leaky gut. 

A leaky gut condition occurs when holes or gaps exist alongside the lining of your gastrointestinal tract. Issues, like those 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 these particles begin circulating throughout your whole 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. (18)


Toxins are everywhere — in our air, food, households, personal care products, water, and more. They are unavoidable and can build up in our body. This leads to inflammation and dysfunction of key systems in the body. Over time, an excess of toxins can contribute to or cause many ailments. 

Biotoxins and environmental toxins are leading contributors to autoimmune diseases and thyroid problems. They can damage proper immune balance, thyroid function, and overall wellness. These toxins include: (19, 2021)

Conventional Medicine vs. Foundational Medicine Approach

Conventional medicine treats Hashimoto’s with thyroid medication that contains synthetic thyroid hormones once hypothyroidism develops — 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 have surgery to remove the gland. (22)

Allopathic medicine views Hashimoto’s disease 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 worlds take a different approach.

A foundational approach looks to find potential root causes of hypothyroidism symptoms. Foundational medicine also works to restore basic drainage and detox function, which can in turn help areas like the thyroid.

Ways to support your body’s foundation include:

Clear Infections

As previously stated, bacterial and parasitic 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. (9)

A holistic, foundational approach can help to tackle all these infections. That approach includes supporting your drainage, detoxification, and immune functions. Some types of support that may help in your fight against opportunistic pathogens include: (23, 24, 25)

  • Drainage support: Drainage pathways in the body “take 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. 
  • Detox support: Your kidneys and liver process the bulk of toxins and send them out in your urine and stools. These organs benefit from extra support for healthy kidney and liver function
  • Minerals: You need minerals like selenium and zinc for healthy immune function that fights infections effectively. 
  • Parasite-fighting support: Parasites are a substantial drain on your immune system. Some also harbor the Lyme bacteria Borrelia and other pathogens. Certain herbs may help you take down the critters. (26)

Clear Toxins

Toxicity significantly contributes to health challenges, including Hashimoto’s thyroiditis. In many cases, the toxicity itself causes the deficiency. (20)

Binders can help limit or decrease toxic burdens. These work like a strong magnet in the body. They hold on tight to toxins and remove harmful substances from your body via your stools. (27, 28, 29, 30, 31, 32, 33, 34, 35, 36)

Heal the Gut 

Several methods exist to heal the gut and balance the microbiome. Several of them were already discussed. They include: (37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47)

  • Avoiding unnecessary medications
  • Binding gut toxins
  • Consuming fermented foods
  • Conquering infections
  • Following a healthy diet
  • Reducing stress
  • Taking a spore-based probiotic

Thyroid-healing Diet

A thyroid-healing diet is low in carbohydrates and high in clean protein, healthy fiber and fats, and plant-based nutrients. Some of the best foods to eat include: (48, 49, 50, 51)

  • Avocados
  • Apple cider vinegar
  • Coconut fat
  • Cooked cruciferous vegetables
  • Fermented foods
  • Lemons and limes
  • Olive oil
  • Olives
  • Organic bone broths
  • Organic grass-fed ghee or butter
  • Pasture-raised animal products
  • Sea vegetables
  • Wild-caught fish

Include dietary aids, foods, or herbs plentiful in: (52, 53, 54, 55, 56, 57, 58, 59, 60, 61)

  • Vitamin A — found in broccoli, carrots, spinach, and sweet potatoes
  • Vitamin D — found in egg yolks, fish liver oils, mushrooms, and wild-caught fish
  • Vitamin E — found in almonds, avocados, peanuts, and sunflower seeds
  • B vitamins — found in leafy greens, legumes, liver, meats, organic eggs, and wild-caught salmon
  • Magnesium — found in green leafy vegetables, nuts, organic dairy, potatoes, quinoa, soybeans, and whole wheat
  • 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 fortified grains, pastured red meats, and some wild-caught seafood

healthy foods for thyroid diet nutrition

You can also focus your diet on fighting autoimmunity. In an autoimmune diet, you eat anti-inflammatory foods and eliminate inflammatory foods.

To limit inflammation, avoid or reduce: (62)

  • Fried foods
  • Lard, margarine, shortening, and trans-fatty acids
  • Processed meats and red meat
  • Refined carbohydrates
  • Soda and other sugary or high-fructose corn syrup beverages

Anti-inflammatory foods to add to your diet include: (62)

  • Avocado, coconut, and olive oils
  • Green leafy vegetables
  • Low glycemic 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 cause 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 sufficient testing for a proper diagnosis and then work toward healing.