Autoimmune Thyroid Disease: Addressing the root causes of this silent epidemic


Autoimmunity is the single most common cause of thyroid dysfunction. So, if your doctor has diagnosed you with hypothyroidism or hyperthyroidism, you may have autoimmune thyroid disease even if your doctor fails to mention the possibility.

Autoimmune disease is three times more prevalent in women than in men. This could be because women experience greater hormone fluctuations both monthly as well as during puberty, pregnancy and menopause. It’s also possible that because women tend to have more fat stores than men, they could collect and store more lipophilic toxins. Additionally, women are historically more prone to dye their hair, paint their nails and use more personal care products, thus increasing their overall toxic exposure.

Though traditional medicine treats autoimmune diseases as if they are distinctly different from one another, the functional medicine model suggests that autoimmune diseases stem from the same underlying causes: a genetic predisposition, hyper-permeability of the mucosal barrier (what is known as leaky-gut syndrome) and the presence of an environmental trigger.

Autoimmunity occurs when a hyper-vigilant immune system cannot distinguish between an invader and the body’s tissues. The specific tissues being attacked determines the diagnosis. When the immune system attacks the myelin sheath, it causes multiple sclerosis; when it attacks the joints, it causes rheumatoid arthritis. If it attacks the thyroid, then either Hashimoto’s or Grave’s disease could follow.

It is common for people to acquire multiple autoimmune diagnoses. For example, someone with celiac disease may end up developing psoriasis and then get diagnosed with Hashimoto’s a few years later. Unfortunately, autoimmunity progresses in silence until enough tissue damage has occurred that symptoms emerge and diagnosis is possible.


There are many triggers for autoimmunity with gluten sensitivity being one of the most common. But even in the absence of gluten sensitivity, gluten consumption can trigger autoimmunity by activating inflammation and promoting leaky gut. Other triggers of thyroid autoimmune disease are:

  • Increased gut permeability (leaky gut)

  • Food sensitivities

  • Heavy metal toxicity

  • Exposure to toxic chemicals

  • Viral infections: EBV, CMV, herpes and Lyme’s disease

  • Bacterial infections: Klebsiella, Yersinia, Citrobacter, E. coli, Proteus, et al.

  • Parasites and opportunistic yeast/fungus

  • Chronic inflammation

  • Chronic stress

  • Nutrient deficiencies

  • Environmental toxic exposures


Hashimoto’s is the most common cause of hypothyroidism and may be responsible for more than 90 percent of hypothyroid cases. Hashimoto’s gets called “hypothyroidism” because the immune system attacks either thyroid peroxidase or thyroglobulin, bringing down thyroid hormone levels and slowing metabolism.

In the early stages, there may be no symptoms present. Sometimes, there can be a period of an overproduction of thyroid hormones before thyroid hormone levels eventually drop. It can take years before enough tissue damage occurs to cause symptoms. 

It is quite common for Hashimoto’s cases to go undiagnosed due to inadequate lab testing but also because there’s little reason for traditional docs to pursue a Hashimoto’s diagnosis when they have no specific treatment options beyond hormone replacement.

This is unfortunate since current research suggests that Hashimoto’s is more prevalent than Type 2 diabetes.

Grave’s disease is the most common cause of hyperthyroidism by about 95 percent over other causes. Having said that, it is far less common than Hashimoto’s and less than three percent of the population is affected. With Grave’s disease, there is an overproduction of thyroid hormone due to the immune system producing thyroid stimulating immunoglobulins (TSI). These immunoglobulins have much the same action as TSH (thyroid-stimulating hormone). They stimulate the TSH receptors and signal the thyroid gland to increase thyroid hormone levels.

Grave’s disease occurs most frequently in women who are in their 30s and 40s.


Because gluten is one of the primary triggers of thyroid autoimmunity, it’s worthwhile to spend some time reviewing just how gluten consumption promotes autoimmunity in general.

For starters, gluten sensitivity is quite common. Celiac disease affects about one percent of the population (roughly one in every 131 people), but one out of every five people is likely to have non-celiac gluten sensitivity (NCGS). 

It’s a common misconception that gluten sensitivity always causes symptoms like diarrhea, cramping, gas and bloating; however, many with celiac disease or NCGS experience NO gastrointestinal symptoms at all, even when significant gut damage is present. Therefore, it’s common for celiac disease and NCGS to go undiagnosed.

Unfortunately, even those who know they are gluten sensitive may not be vigilant about avoiding gluten unless they experience immediate and severe GI reactions. They are more likely to cheat here and there thinking that a little bit now and then can’t hurt. But one small exposure to gluten can set off an inflammatory response that can last six months or more.

Gluten is a prolamin form of lectin that triggers a mild-to-severe inflammatory reaction in the body, compromising digestion and disrupting immune function. Regardless of one’s sensitivity level, gluten promotes leaky gut in everyone. Not only does gluten damage the villi and microvilli of the gut lining, but it also triggers a rise in zonulin. Zonulin is an enzyme that regulates the tight junctions between the enterocytes of the gut lining. As zonulin levels rise, the tight junctions open, allowing unwanted organisms, food antigens, toxins and immune globulins to leak through and make their way into the bloodstream.

Gluten is one of the most common allergenic foods and can trigger mild-to-nagging inflammatory conditions throughout the body. Long-term gluten consumption may result in joint pain, various skin conditions, chronic headaches, acid reflux and other digestive complaints along with anxiety, depression and other neurological symptoms.

Studies suggest that almost half of the people with gluten sensitivity will eventually acquire some type of thyroid disorder. 


When a gluten protein passes through a leaky gut, the immune system responds by tagging it for identification and destruction. Antibodies to this invader are produced and they roam the body looking for gluten proteins to destroy. Unfortunately, the structure of the gluten protein is so similar to thyroid tissue that the immune system will often attack the thyroid to eradicate gluten.

Wheat germ agglutinin (WGA) is a lectin aspect of wheat that can infiltrate the bloodstream due to its tendency to punch holes in the gut lining. When WGA circulates through the body, it can attach to various organ tissues while exciting the immune system. When the immune system does battle with WGA, any surrounding tissue gets damaged in the process.

Studies suggest that almost 100 percent of people diagnosed with Hashimoto’s are either non-celiac gluten sensitive or have celiac disease.

It is also important to note that BOTH celiac disease and NCGS may be directly linked to ALL autoimmune disorders. And there is no such thing as being “a little” sensitive to gluten. If you have an autoimmune disease, you should never eat gluten. Full stop.


If you’ve been diagnosed with hypothyroidism, or even Hashimoto’s, you have likely been given a prescription for a synthetic hormone replacement (Synthroid, Levothyroxine, Cytomel, et al.) or perhaps a desiccated thyroid product like Armour or Nature Throid. The reasoning is simple: When thyroid-hormone levels are low and the patient is experiencing negative symptoms, a thyroid-hormone replacement can bring levels back to a normal level and make the patient feel better. Case closed.

In the case of hyperthyroidism, or Grave’s Disease, the thyroid gland is producing too much hormone and is usually enlarged. Treatment options are varied and may include the administration of radioactive iodine, anti-thyroid medications or a thyroidectomy. 

Radioactive iodine causes the thyroid gland to shrink and become less active. While this treatment can alleviate hyperthyroid symptoms, it can also cause a state of hypothyroidism that requires the patient to take a synthetic or desiccated hormone replacement. Anti-thyroid medications prevent the thyroid gland from producing excess thyroid hormones but are also known to cause liver damage, allergic reactions and infection. The final option is a thyroidectomy—the surgical removal of the thyroid gland. For obvious reasons, this option requires patients to take thyroid hormone replacement for the rest of their lives.

The trouble with all these treatments is that they are focused on symptom alleviation and hormone regulation only and do nothing to address the underlying causes of your thyroid disorder. And since there are no treatments specific to thyroid autoimmunity, there is a tendency toward under-diagnosis.


Addressing thyroid autoimmunity is a four-step process: remove, replace, restore and regulate.

Step 1 –  Removal of triggers that are causing and exacerbating your disease 

We have already discussed that gluten is one of the most common triggers for thyroid autoimmunity, so it should come as no surprise that eliminating gluten from your diet is a must. Still, there may be other triggers that need to be identified and eliminated. I suggest working with a licensed or certified functional practitioner who will recommend the appropriate lab tests and guide you through the process. In my clinical experience, there is no singular trigger; rather, each client has their own “perfect storm” of triggers and all must be resolved before real healing progress is made.

Removing triggers helps to slow tissue destruction and to lower antibody levels when they are elevated. In addition to removing triggers, supplementation with selenium, inositol and/or proteolytic enzymes has been shown to reduce thyroid antibodies and ease symptoms of an autoimmune flare.

Step 2 – Replacement of missing nutrients

Another thing to consider when evaluating thyroid health is whether there are underlying nutritional deficiencies that may need to be addressed. Keeping in mind, of course, that what we eat and what we absorb may be two different things. Nutrient absorption can be impacted by many health issues like low stomach acid, impaired enzyme production, gut pathogens, imbalances of healthy gut flora, inflammation of the mucosal lining and leaky gut. 

There are specific nutrients that directly impact thyroid function. Vitamin B12, magnesium, zinc and adequate protein intake are required to produce TSH (the signal that tells your thyroid to produce thyroid hormones). Selenium is necessary for thyroid-hormone conversion, and some studies suggest that it may also help reduce thyroid antibodies. The production of T4 relies upon adequate iodine levels as well as vitamin C and vitamin B2. Where iodine is concerned, vitamin B6 is required for proper utilization and absorption. A word of caution when it comes to iodine: Any sudden increase in iodine levels can exacerbate thyroid autoimmunity and drive up antibody levels. Adequate iron levels are necessary to support the action of thyroid peroxidase and TSH as well as the production of thyroid hormone. 

It’s common for iron deficiency and iodine deficiency to go hand-in-hand. The fat-soluble vitamins D and A support thyroid hormone receptors and, as already mentioned, vitamin D is critical for proper immune function. There is a correlative relationship between low vitamin D levels and autoimmunity. Anyone with an autoimmune disease should get their vitamin D levels checked regularly. Finally, a deficiency in vitamin E can worsen an imbalance of Th1 and Th2 pathways and contribute to an overall reduction in thyroid hormone.

Nutritional note: Goitrogenic fruits and vegetables and soy products may interfere with the thyroid peroxidase enzyme and drive down thyroid hormone production. Having said that, cooking goitrogenic foods does help to mitigate this effect.

To properly assess whether nutrient deficiencies play a role in your thyroid disorder, I recommend seeking the guidance of a functionally trained practitioner who is experienced at analyzing the tests most suited for this purpose. 

Step 3 – Restoring the integrity of the gut lining

Since a leaky gut sets the stage for all autoimmune disorders, it is common sense that we need to heal the gut lining to halt, slow or reverse the disease process. Restoration of the gut involves removing the triggers that promote leaky gut, which are gluten, glyphosate, heavy metals, parasites, opportunistic bacterial infections, yeast overgrowth and more. Healing the gut also involves the strategic use of various nutrients and herbs that promote healing of the intestinal epithelium.

Step 4 – Regulating the immune system

Regulating the various pathways of the immune system is the key to managing thyroid autoimmunity. Without getting too nerdy, let’s review the main points of immune function that concern us. Immune pathways are governed by specific types of cells that either promote or inhibit inflammation, antibody production and overall immune response. 

T-reg cells are immunosuppressive and modulate the immune system to maintain tolerance to self-antigens. We want to support these guys. Low vitamin D levels will compromise T-reg function and increase the risk of autoimmune disease and allergic reactions. Maintaining adequate levels of vitamin D is critical for T-reg support. Other nutrients and compounds that support T-reg function are omega-3 fatty acids (fish oil) and glutathione, the body’s master antioxidant.

There are three “immune pathways” that warrant discussion. Each pathway releases its own unique blend of inflammatory cytokines associated with different aspects of the immune response.  

Th17 cells—which govern the Th17 pathway—are pro-inflammatory and linked to several autoimmune diseases such as Hashimoto’s, psoriasis, rheumatoid arthritis, multiple sclerosis, Crohn’s disease and ulcerative colitis. These cells also provide a strong link between celiac disease and Hashimoto’s. Obviously, we want to calm this pathway down. It is important to note that specific gut infections (parasites, bacteria and yeast) and viruses, like Lyme disease, increase Th17 levels—another reason why you’ll want to work with a functionally trained practitioner.

Strategies to bring down Th17 levels and dampen the Th17 pathway: 

  • Remove inflammatory triggers – inflammatory foods, processed and sugary foods, alcohol, etc. Resist inflammatory lifestyle behaviors such as lack of sleep and excessive mental/emotional stress. 

  • Identify and eliminate gut infections.

  • Introduce anti-inflammatory nutrients and compounds such as curcumin, boswellia, pancreatic enzymes and high-quality probiotics.

That brings us to Th1 and Th2 pathways. General health is optimized when these pathways are in balance with one another. But often, one of these pathways tends to dominate the other due to the presence of an autoimmune disease or other factors like viral and gut infections, food sensitivities and blood-sugar dysregulation.

Th1 cells, which govern the Th1 pathway, are mostly involved with the immediate immune response whereas Th-2 cells, which govern the Th2 pathway, are more involved with the delayed immune response. The dominance of either pathway can accelerate the progression of autoimmune disease because Th1 dominance tends to increase tissue damage and Th2 dominance increases antibody production. Both pathways will produce inflammatory cytokines that block thyroid cell receptors.

Though there is no hard and fast rule to determine which pathway is dominant in a person, there are some general guidelines.  Th1 dominance is linked to irritable bowel syndrome, rheumatoid arthritis, celiac disease, psoriasis, Crohn’s disease, multiple sclerosis, Type 1 diabetes, Alzheimer’s, polycystic ovarian syndrome and lupus. Th2 dominance is linked to asthma, eczema, histamine intolerance, Grave’s disease, hives, Sjogren’s syndrome and IgE allergies. Keep in mind, though, it is quite common for people to have health issues that are associated with both pathways.

The first step in balancing the Th1 and Th2 pathways is to support immune modulation and bring down inflammation. All the strategies for T-reg support and Th17 control will help in this effort. Additionally, supplements such as colostrum, high-quality probiotics and vitamins A and E will aid in immune modulation. Colostrum can be problematic for those with dairy sensitivity in which case serum-derived immunoglobulins are good replacements. Finally, certain nutrients and compounds can be taken to support whichever pathway is NOT dominant. 

  • Upregulate the Th1 pathway: astragalus, echinacea, licorice, thymus, spleen, parotid, vitamins A and C, zinc.

  • Upregulate the Th2 pathway: green-tea extract, grape-seed extract, pine-bark extract, maritime-pine extract, resveratrol.


In addition to implementing the Four R’s, it may still be necessary to take thyroid-hormone replacement medication. Synthetic hormone replacements such as Synthroid, Cytomel and Levothyroxine are well-known options and may get the job done for many. But they also may contain inactive ingredients that interfere with absorption (magnesium stearate, colloidal silicon dioxide, artificial colors, microcrystalline cellulose, et al.) or that make thyroid autoimmunity worse (gluten and corn). I often recommend that my clients speak with their prescribing physician about trying WP Thyroid, a natural desiccated thyroid (NDT) product. Other NDT products like Nature Throid and Armour may be less effective than WP Thyroid because they contain more inactive ingredients. Thyro-Gold, a non-prescription product made from the thyroid glands of grass-fed, New Zealand cattle, is also a viable option to be discussed with your doctor. 


Obtaining true and lasting improvement in thyroid health usually requires that you go deeper. Working with a functional practitioner is the most direct route toward deep healing. Functional practitioners like myself are not in the business of just alleviating symptoms. Instead, the goal is to uncover the underlying imbalances and hidden dysfunctions that are at the root of your thyroid disorder and then develop customized healing strategies to correct them.

Functional practitioners use specialized lab tests to take a deep dive into your health issues, uncovering the root causes that drive your symptoms. Proper testing is the only way to identify:

  • Leaky gut

  • Hidden food sensitivities

  • Heavy-metal toxicity

  • Impairment of detox pathways

  • Nutrient deficiencies

  • Gut infections & dysbiosis – parasites, bacteria and yeast

  • Chronic viral infections

  • Mold and mycotoxins

  • And much more….

Just one or two underlying imbalances or hidden dysfunctions are enough to hijack all your efforts to adequately address thyroid dysfunction.

To learn more about Functional Diagnostic Nutrition® or to inquire about working with me, please visit

If you suspect you have a thyroid condition but haven’t yet had your thyroid tested, or maybe you’ve been told that all your thyroid numbers are normal but you still have all the symptoms of a thyroid disorder, then you might want to check out my blog post regarding thyroid testing and assessment: So Your Thyroid Labs are Normal but You Feel Like Crap?