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Uncovering the Causes of Hashimoto’s Thyroiditis

By Stephanie Deppe, M.D.

It is estimated that 12% of people in the U.S. will have a thyroid disorder at some point during their lifetime (1). Iodine deficiency is the leading cause worldwide for hypothyroidism. However, in the US, 90% of people diagnosed with hypothyroidism have the autoimmune thyroid disease, Hashimoto’s thyroiditis (2). A typical scenario might go like this... you present to your doctor with symptoms of fatigue, lethargy, weight gain. He or she tests your TSH and finds that it’s high with a low T4 level. You’re told you have hypothyroidism and that it’s probably due to Hashimoto’s (or hopefully your doctor will actually check antibodies to confirm). You’re placed on a thyroid medication with no further investigation or discussion as to the driving cause.

As an allopathically trained physician, I understand why there is little discussion around such a common health problem. Physicians don’t receive adequate training during medical school about potential causes of Hashimoto’s or treatment beyond medication. Your doctor means well, but he or she may not realize or simply doesn’t have the time to discuss the upstream triggers for Hashimoto’s and ways to reverse this disease at its origins.

What is Hashimoto’s?

Hashimoto’s is an autoimmune attack on the thyroid gland that destroys the cells that make thyroid hormones. It leads to symptoms of hypothyroidism such as fatigue, lethargy, brain fog, sluggishness, feeling cold, menstrual irregularities, infertility, weight gain, dry skin, hair loss, constipation, and more. About 90% of people with Hashimoto’s have antibodies to TPO (thyroid peroxidase)--an enzyme that converts dietary iodine into thyroid hormones. About 80% of people have antibodies to thyroglobulin–another thyroid protein that is also involved in thyroid hormone production (2). Typically, these antibodies are not checked unless a patient’s labs fall outside of the “normal” reference range for TSH (0.5-5.0 mIU/L). However, these ranges are probably too broad for healthy individuals. They were designed to include the elderly and those people with undetected thyroid dysfunction. A desirable TSH level in the functional medicine realm is typically 0.2-2.5 mIU/L. It is possible to have labs in the conventionally “normal” range, and still have positive thyroid antibodies.

What Causes Hashimoto’s?

There isn’t one clear trigger for Hashimoto’s, but research shows that genes do play a role. Roughly half of siblings of patients with Hashimoto’s disease also tested positive for thyroid antibodies, but this didn’t mean that those siblings developed symptoms or had abnormal TSH values (3). We know that there are probably multiple environmental factors that trigger the disease. In functional medicine, we try to identify these triggers and fix them where they start. Frequently, we may see issues with gut health (microbiome balance and intestinal infections), intestinal permeability (“leaky gut”), chronic infections, nutrient deficiencies, iodine excess, chronic stress, toxin exposure, and gluten sensitivity.

The Role of Iodine

Iodine is required to make thyroid hormones, and deficiency is the leading cause of hypothyroidism worldwide. However, iodine intake has a sweet spot when it comes to thyroid health. In the 1920s, iodine began to be added to commercial salt products in the U.S. to fix this issue (4). The strategy was effective, and hypothyroidism secondary to iodine deficiency now makes up less than 10% of hypothyroid cases in the U.S. (2). Despite this success, rates of Hashiomotos’ thyroiditis began to rise. We see that in countries where iodine intake is adequate, Hashimoto’s is the leading cause of hypothyroidism (5).

Excess iodine intake can actually increase the autoimmune attack on the thyroid gland. This probably occurs through increased thyroid peroxidase (TPO) enzyme activity in the thyroid and the production of inflammatory substances that occurs when iodine is metabolized (6). One study actually showed that iodine restriction reversed Hashimoto’s disease in 78% of the participants (7). However, it would be irresponsible to make a blanket statement that all people with Hashimoto’s should avoid iodine. Iodine supplementation may be necessary, and testing for iodine with a 24-hour urine provocation test after an iodine loading dose can help clarify. It should also be noted that selenium should always be given with iodine, as not replacing this important mineral can actually increase thyroid inflammation. If you are struggling with Hashimoto’s, I would recommend discussing the topic of iodine with an experienced practitioner.

So how much iodine is adequate for general thyroid health if you do not have Hashimoto’s? The recommended dietary intake for adults is 150 micrograms/day, and more for pregnant and breastfeeding women (8). I would not recommend eating table salt to meet your iodine intake. Celtic sea salt is not fortified with iodine. Better sources of iodine include fish and shellfish, eggs, chicken, liver and dairy (9). Seaweed is an incredibly rich source of iodine. One option is to season food with kelp granules a couple of times per week. I recommend that everyone take a high-quality multivitamin, which often also contains iodine.

Other Ways to Support Your Thyroid Health

The thyroid requires several vitamins and minerals to function properly. Conversion of T4 (the thyroid storage hormone) into T3 (the active hormone) requires zinc and selenium. Food sources rich in zinc include oysters, beef, liver, and chicken. Your daily intake of selenium can be accomplished simply by eating two brazil nuts per day. Selenium is also important for clearing the inflammatory substances that are made when the thyroid metabolizes iodine (2). Other antioxidants that help reduce inflammation and improve thyroid function include vitamin C, glutathione and its precursor N-acetyl cysteine, and vitamin E.

It’s important to ensure your gut is working optimally. Damage to the gut lining (resulting in intestinal permeability) can impair nutrient absorption and increase exposure to toxic substances. Furthermore, intestinal permeability may actually be a trigger for autoimmune thyroid disease. The tight connections between intestinal cells keep out incompletely digested food particles and foreign substances. These junctions can be damaged by infections, chronic stress, prescription medications, yeast overgrowth, dysbiosis, and even gluten (10, 11). It has been suggested that when foreign materials escape freely from the gut into the bloodstream, they induce an inflammatory response wherein the immune cells may mistake the body’s own thyroid tissue as the problem, which leads to an autoimmune attack (2). Gluten is known to trigger intestinal permeability, and so I always recommend that patients with autoimmune thyroid disease eliminate gluten while working on their underlying disease triggers (11).

A discussion of root cause evaluation for thyroid dysfunction would not be complete without also addressing adrenal health. The adrenal glands make cortisol and other stress hormones in response to internal or external stressors. Elevated cortisol increases reverse T3 and reduces the conversion of T4 to T3 (the active hormone). I test cortisol levels in the majority of my patients, and I would say that 9 out of 10 of my patients have some degree of adrenal dysregulation! I always recommend testing and treating any adrenal problem when running a thyroid program.

The Role of Thyroid Medication

Prescription thyroid replacement is often needed for patients with Hashimoto’s disease. Most commonly, patients are prescribed levothyroxine (T4 hormone), such as Synthroid. This is often adequate, but some people are inefficient at converting T4 into T3 (the active hormone), which results in inadequate symptom control. Other patients may have sensitivities to fillers in these medications. Tirosint is a gel cap version of T4 that is free from additives, which can be a good alternative to Synthroid for these individuals. Other options include desiccated pork thyroid (such as Armour and Nature-throid)--which contains both T4 and T3–, the addition of synthetic T3 (Cytomel) to T4, or using compounded thyroid hormone instead.

In addition to thyroid medication, some patients are using low-dose naltrexone (LDN). LDN has been found to favorably influence immune system activity and reduce inflammation in multiple autoimmune conditions. We still don’t know whether or not LDN works for Hashimoto’s, although there are several case reports of positive effects (12). Until we have more research on LDN and Hashimoto’s, it’s hard to know if it’s effective across the board but is an interesting topic of conversation and area for future investigation.

I hope this information helps you or a loved one. The content of this article is informational only and is not meant to diagnose or treat your specific condition. I always recommend working with an experienced functional medicine practitioner to achieve your individual health goals.

To your health,

Dr. Deppe


  1. American Thyroid Association. (2016). General Information/Press Room | American Thyroid Association. [online] Available at:

  2. Wentz, I. and Nowosadzka, M. (2015). Hashimoto’s thyroiditis : lifestyle interventions for finding and treating the root cause. United States? Izabella Wentz.

  3. Zaletel, K. and Gaberscek, S. (2011). Hashimotos Thyroiditis: From Genes to the Disease. Current Genomics, [online] 12(8), pp.576–588. doi:10.2174/138920211798120763.

  4. Leung, A., Braverman, L. and Pearce, E. (2012). History of U.S. Iodine Fortification and Supplementation. Nutrients, [online] 4(11), pp.1740–1746. doi:10.3390/nu4111740.

  5. Chiovato, L., Magri, F. and Carlé, A. (2019). Hypothyroidism in Context: Where We’ve Been and Where We’re Going. Advances in Therapy, 36(Suppl 2), pp.47–58. doi:10.1007/s12325-019-01080-8.

  6. Chung, H.R. (2014). Iodine and thyroid function. Annals of Pediatric Endocrinology & Metabolism, [online] 19(1), p.8. doi:10.6065/apem.2014.19.1.8.

  7. Yoon, S.-J., Choi, S.-R., Kim, D.-M., Kim, J.-U., Kim, K.-W., Ahn, C.-W., Cha, B.-S., Lim, S.-K., Kim, K.-R., Lee, H.-C. and Huh, K.-B. (2003). The effect of iodine restriction on thyroid function in patients with hypothyroidism due to Hashimoto’s thyroiditis. Yonsei medical journal, [online] 44(2), pp.227–35. doi:10.3349/ymj.2003.44.2.227.

  8. National Institutes of Health (2017). Office of Dietary Supplements - Iodine. [online] Available at:

  9. Boston, 677 H.A. and Ma 02115 +1495‑1000 (2021). Iodine. [online] The Nutrition Source. Available at:

  10. Bischoff, S.C., Barbara, G., Buurman, W., Ockhuizen, T., Schulzke, J.-D., Serino, M., Tilg, H., Watson, A. and Wells, J.M. (2014). Intestinal permeability – a new target for disease prevention and therapy. BMC Gastroenterology, 14(1). doi:10.1186/s12876-014-0189-7.

  11. Hollon, J., Puppa, E., Greenwald, B., Goldberg, E., Guerrerio, A. and Fasano, A. (2015). Effect of Gliadin on Permeability of Intestinal Biopsy Explants from Celiac Disease Patients and Patients with Non-Celiac Gluten Sensitivity. Nutrients, [online] 7(3), pp.1565–1576. doi:10.3390/nu7031565.

  12. LDN Research Trust. (n.d.). LDN Research Trust. [online] Available at: [Accessed 26 Jul. 2022].

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