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Underlying causes of Hashimoto’s thyroiditis

It is estimated that 20 million Americans have some form of thyroid disease, and up to 60% of those individuals don’t even know they have it.1 Symptoms of thyroid disease are often non-specific and many providers don’t run the proper tests to make an accurate diagnosis. With lifestyle modifications and supplements, it’s possible to support the thyroid gland and prevent or reverse symptoms of thyroid disorders. This blog will focus on the functional medicine approach to Hashimoto’s thyroiditis, the most common cause of hypothyroidism in the United States.

What is Hashimoto’s?

Hashimoto’s thyroiditis, an autoimmune condition, involves chronic inflammation of the thyroid gland due to attack by the body’s own immune system. As the condition progresses, often over the course of many years, thyroid function tends to decline, leading to hypothyroidism. Hashimoto’s is four to ten times more common in women than men and typically appears during midlife but can be seen at any age, and can also affect men and children.2

There are no symptoms specific to Hashimoto’s, but rather are due to the progression to hypothyroidism. These include fatigue, unexplained weight gain, sensitivity to cold, constipation, dry skin, muscle pain, depression, loss of the outer third of eyebrow, and heavy or irregular periods. Some individuals develop a goiter, an enlarged thyroid, that may cause neck discomfort or difficulty swallowing.2

Many times, Hashimoto’s goes undetected or undiagnosed for long periods of time, especially without proper thyroid testing. Most doctors only test thyroid stimulating hormone (TSH) when screening for a thyroid disorder. Not only does TSH alone not provide a complete picture of a person’s thyroid function but it can also be misleading since levels may fluctuate. A person with Hashimoto’s can actually swing between both hypo- and hyperthyroidism. Furthermore, damage to the thyroid may begin long before abnormal TSH (and thyroid hormone) levels are detected. 

When evaluating for a thyroid disorder, functional medicine considers an individual’s medical and family history, a complete physical exam, and a full thyroid panel to include TSH, free T4, free T3, reverse T3 (RT3), total T3, and thyroid antibodies (thyroid peroxidase (TPO) and thyroglobulin antibodies).

Conventional medicine focuses on symptom improvement by supplementing with thyroid medication, typically for life. Although this does not address any underlying causes, it may be an important first step to help the patient feel better. Taking medication while continuing to uncover and correct contributing factors can provide much more relief than medication alone and can even reverse disease.

Underlying causes of Hashimoto’s

There are certain environmental factors that can trigger or underlie the development of Hashimoto’s. If you have a family history of the disease, have thyroid antibodies, or begin to develop signs and symptoms of hypothyroidism, evaluating and correcting the triggers below can help to prevent damage (or prevent further damage) to the thyroid and even reverse disease in some cases.

Intestinal permeability

The gut houses the majority of our immune system so it’s no wonder that increased intestinal permeability (aka “leaky gut”) is a common factor in autoimmune disease. We have a blog post titled Intro to “leaky gut”- what it is and why you should care on our website that does a great job of detailing why leaky gut is so problematic. Essentially, when the intracellular tight junctions of the intestinal mucosal cells become loose (“leaky”), substances are able to pass from the intestinal lumen into the bloodstream where they shouldn’t be. The immune system views these substances as foreign and mounts an immune response, causing inflammation and damage that can eventually lead to chronic disease and autoimmunity. Restoring gut function to include optimal digestion, absorption, a balanced microbiome, and a healthy gut lining can calm down an overactive immune system. This is vital to improving any autoimmune condition, including Hashimoto’s.


Autoimmune diseases in general are linked to various infections, and there are numerous bacteria, viruses, and parasites that have been linked to the development of Hashimoto’s thyroiditis. Some of the more common ones include Epstein-Barr virus (EBV), hepatitis C, H. pylori, Yersinia enterocolitica, Borrelia burgdorferi, Mycoplasma, and Candida.3 It’s advised to work with a skilled practitioner to identify chronic infections and eradicate them as needed.

Environmental pollutants

There are over 80,000 chemicals registered for use in the United States, with an estimated 2,000 new ones added each year.4 These chemicals are found practically everywhere- food, cookware, cleaning supplies, personal care products, lawn care products, household items, and more. One class of chemicals, called endocrine-disrupting chemicals (EDCs), interfere with hormones in the body through various mechanisms (production, release, transport, metabolism, binding, and elimination).5 EDCs exert their effects along the entire hypothalamus-pituitary-thyroid (HPT) axis, directly or indirectly affecting other hormonal systems and wreaking havoc throughout the body. Common EDCs include persistent organic pollutants, bisphenol A (BPA), phthalates, and pesticides.5  Although it’s impossible to completely avoid exposure to these chemicals, there are lifestyle strategies you can employ, such as switching to safer products and supporting your body’s detoxification pathways, to greatly reduce exposure and any potential harmful health effects. Our blog post Detoxification: Part 2 provides examples to help you identify and remove sources of exposure.


Chronic inflammation is a hallmark characteristic of most chronic disease and autoimmune disorders that are prevalent today. There are many different sources of inflammation- the standard American diet, food sensitivities or intolerances, gut dysbiosis, chronic stress, environmental toxins, stealth infections, and disturbed sleep.6 Increased inflammation in the body decreases active thyroid hormone levels. To restore balance, it’s imperative to promote an anti-inflammatory environment. Identifying and removing inflammatory triggers will provide relief to a dysregulated immune system.

Other autoimmune diseases

Having autoimmune thyroid disease (AITD) puts an individual at risk of developing other autoimmune disorders.7 The term polyautoimmunity has been used to describe an individual with more than one autoimmune disease. One study found that AITD was the most common autoimmune disease (AD) to coexist in a select group of patients that had other ADs (systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and systemic sclerosis).8 Another study found that 53% of patients in an endocrinology clinic that had thyroid autoimmune disease (TAD) had coexistent AD or antibodies commonly found in other ADs.9 Reducing inflammation and improving immune health can help slow the progression of Hashimoto’s and prevent the development of other ADs.

Bottom Line

Prevention of disease should always be the goal but there is hope for those already diagnosed with Hashimoto’s. Working with a functional medicine provider to address the factors mentioned above can help prevent further damage to the thyroid, restore function, minimize symptoms and even put autoimmune disease into remission for some.

Our pharmacists at PharmToTable specialize in functional medicine using a lifestyle-based approach and we also have health coaches on our team who can help you make changes towards improving your health. We’d be honored to help you on your journey of improving Hashimoto’s or other thyroid disorder. Book an appointment or schedule a free 15-minute discovery call today!

**Throughout January and February 2022, our Table Talk membership sessions will be centered around the book Hashimoto’s Thyroiditis: Lifestyle Interventions for Finding and Treating the Root Cause by Izabella Wentz, PharmD. These discussions will be a great way to learn more about thyroid disease, listen to our pharmacists share ways to improve thyroid health, and get your health questions answered. Join us here for our thyroid health Table Talk and get your first 2 sessions FREE!

Written by Megan Morrison, PharmD


  1. American Thyroid Association. General Information/Press Room. Accessed January 3, 2022.
  2. Hashimoto’s Disease. National Institute of Diabetes and Digestive and Kidney Diseases. Accessed January 3, 2022.
  3. Dittfeld A, Gwizdek K, Michalski M, Wojnicz R. A possible link between the Epstein-Barr virus infection and autoimmune thyroid disorders. Cent Eur J Immunol. 2016;41(3):297-301. doi:10.5114/ceji.2016.63130
  4. National Toxicology Program. Catalog of Environmental Programs 2012. Accessed January 3, 2022.
  5. Papalou O, Kandaraki EA, Papadakis G, Diamanti-Kandarakis E. Endocrine Disrupting Chemicals: An Occult Mediator of Metabolic Disease. Front Endocrinol (Lausanne). 2019;10:112. Published 2019 Mar 1. doi:10.3389/fendo.2019.00112
  6. Furman, D., Campisi, J., Verdin, E. et al. Chronic inflammation in the etiology of disease across the life span. Nat Med 25, 1822–1832 (2019).
  7. Bliddal S, Nielsen CH, Feldt-Rasmussen U. Recent advances in understanding autoimmune thyroid disease: the tallest tree in the forest of polyautoimmunity. F1000Res. 2017;6:1776. Published 2017 Sep 28. doi:10.12688/f1000research.11535.1
  8. Rojas-Villarraga A, Amaya-Amaya J, Rodriguez-Rodriguez A, Mantilla RD, Anaya JM. Introducing polyautoimmunity: secondary autoimmune diseases no longer exist. Autoimmune Dis. 2012;2012:254319. doi:10.1155/2012/254319
  9. Betterle C, Zanchetta R. Update on autoimmune polyendocrine syndromes (APS). Acta Biomed 2003;74:9-33.
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