Thyroid Health Protocol: A Resource for Practitioners


Written and medically reviewed by Fullscript’s Integrative Medical Advisory Team

First described by Hakaru Hashimoto in 1912, (25) Hashimoto’s thyroiditis is the most common cause of hypothyroidism in developed countries, including the United States where it affects approximately 1-2% of the population. (4)(25) Although the condition can occur in both men and women at any age, it is at least ten times more common in women and most often diagnosed between the ages of 30 to 50 years old. (14)

What is Hashimoto’s thyroiditis?

Hashimoto’s thyroiditis, also known as Hashimoto’s disease, chronic lymphocytic thyroiditis, or autoimmune thyroiditis, is a progressive autoimmune disease resulting in damage to the thyroid gland and ultimately, hypothyroidism. (17) In individuals with Hashimoto’s, the body produces antithyroid antibodies that destroy cells of the thyroid gland resulting in decreased production of thyroid hormones. (7)(14)(17) Thyroid hormones play a key role in energy metabolism (17) and regulation of several vital body functions, such as growth and development, heart rate, body weight, body temperature, and menstrual cycles. (4)

woman holding her neck

Hashimoto’s thyroiditis is a progressive autoimmune disease resulting in damage to the thyroid gland and ultimately, hypothyroidism.

Causes and risk factors

While the pathogenesis and the exact cause of Hashimoto’s thyroiditis are not fully understood, it is believed that the condition involves a combination of genetic susceptibility and environmental triggers. (17)(25) Research has identified the involvement of a number of possible genes, including those involved in the human leukocyte antigen (HLA) complex and in the regulation of immune and thyroid function. It has been suggested, however, that these genetic variations only account for a very small increase in the overall risk. (4)

Many other factors may contribute to an individual’s risk of developing Hashimoto’s, including:

  • Having a close relative with Hashimotos (4)(17)
  • Gender (more common in women)
  • Changes in sex hormones (particularly in women)
  • Exposure to ionizing radiation (4)
  • Infections (e.g, hepatitis C infection, parvovirus, rubella, herpes simplex virus, Epstein Barr virus, and human T-
  • lymphotropic virus type 1, Toxoplasma gondii)
  • Certain medications (e.g., IFN-α, IL-2)
  • Excess consumption of iodine (4)(29)
  • Chemical exposure (e.g., polyaromatic hydrocarbons or polyhalogenated biphenyls) (29)

Further, Hashimoto’s thyroiditis is commonly associated with other autoimmune conditions, including Addison’s disease, diabetes mellitus type 1 (T1DM), rheumatoid arthritis, systemic lupus erythematosus (SLE), autoimmune hepatitis, pernicious anemia, Sjögren’s syndrome, vitiligo, and multiple sclerosis. (4)(17)(25)

Signs, symptoms, and complications

Hashimoto’s thyroiditis is typically diagnosed based on symptoms, a physical exam, and blood tests indicating elevated thyroid-stimulating hormone (TSH), low “free” thyroxine (T4), and increased anti-thyroid peroxidase (anti-TPO) antibodies (7)(14)

Signs and symptoms of Hashimoto’s, which develop and progress over time, include:

  • Goiter (will disappear as the condition progresses)
  • Difficult swallowing
  • Fatigue
  • Thin, brittle hair and skin
  • Hair loss
  • Weight gain, difficulty losing weight
  • Slow heart rate
  • Joint and/or muscle pain
  • Pale, puffy face
  • Cold intolerance
  • Constipation
  • Heavy and/or irregular menstrual cycles (women)
  • Difficulty conceiving (women)
  • Difficulty concentrating or thinking (4)(7)

If left unaddressed, individuals with Hashimoto’s may develop several serious complications, including:

  • Goiter, which may interfere with swallowing or breathing
  • Enlarged heart or heart failure
  • Depression and slowed mental functioning
  • Decreased libido
  • Myxedema coma
  • Birth defects (if mother has untreated hypothyroidism) (7)
woman wrapped in a blanket looking at her laptop

Signs and symptoms of Hashimoto’s may include cold intolerance and fatigue.

Integrative protocol for thyroid health

The conventional treatment for Hashimoto’s thyroiditis typically involves hormone replacement therapy. (17) For example, levothyroxine is a medication commonly prescribed for thyroid hormone deficiency, including Hashimoto’s-related deficiency. (14) The following protocol, used on its own or in conjunction with other treatments, contains nutrients that have been shown to induce beneficial effects on thyroid function.


An essential trace element, (18)(20)(24) selenium is an important component of several selenoproteins, such as glutathione peroxidase, (20) that participate in critical body functions, including DNA synthesis, reproduction, immune responses, and thyroid hormone metabolism. As a result, selenium may play a role in a number of health conditions, such as cardiovascular disease, cancer, cognitive decline, and thyroid disease. (18)

Selenium is naturally present in a wide variety of dietary sources. Common animal sources include organ meats, beef, poultry, dairy, fish, and other seafood. Plant-based sources of selenium include nuts, particularly Brazil nuts, seeds, green vegetables, grains, and certain mushrooms. When choosing plant-based foods, it’s important to note that selenium content can vary significantly depending on the content of the soil in which these foods are grown. (18)(24)

Research findings:

  • A decrease between 20% and 63.6% in anti-TPO marker has been observed (2)(12)(23)(28)

US: Search for Selenium in the Fullscript catalog.
CAN: Search for Selenium in the Fullscript catalog.

a variety of raw food including nuts, seeds, meats, seafood and more

Common dietary sources of selenium include organ meats, seafood, Brazil nuts, seeds, and certain mushrooms.

Vitamin D

Vitamin D is a prohormone and a non-essential, fat-soluble vitamin (5) that can be synthesized endogenously by the skin with exposure to ultraviolet rays from sunlight. In addition to endogenous production, vitamin D in the form of vitamin D3 and its metabolite 25(OH)D3 may be obtained from certain foods, such as fatty fish (e.g, salmon, mackerel, tuna), beef liver, dairy, and egg yolks. Another form of the vitamin, vitamin D2, can be found in variable amounts in mushrooms. (19)

Vitamin D is well-known for its role in maintaining bone health by promoting calcium absorption and bone mineralization. Vitamin D is involved in other key body functions, such as supporting neuromuscular and immune function, reducing inflammation, and regulating cell growth, proliferation, differentiation, and apoptosis. (19)

It is estimated that vitamin D deficiency affects approximately 1 billion people worldwide. Vitamin D deficiency is a risk factor for total mortality (15) and has been associated with several health conditions, including osteoporosis, muscle weakness, rheumatoid arthritis, diabetes, hypertension, cancer, multiple sclerosis, (30) and Hashimoto’s thyroiditis. (27)

Research findings:

  • It has been demonstrated that low levels of serum 25-hydroxyvitamin D are related to thyroid auto-immune conditions like Hashimotos (27)
  • Vitamin D has been shown to decrease concentrations of thyroid peroxidase and thyroglobulin antibodies (8)(9)(13)
  • Vitamin D has been linked to a decrease in thyroid autoimmunity in Hashimoto’s thyroiditis treated with levothyroxine. The impact is more significant for thyroid peroxidase than thyroglobulin antibodies (8)
  • The combination of Simvastatin and vitamin D supplementation had a stronger effect in reducing concentrations of thyroid peroxidase and thyroglobulin antibodies then vitamin D supplementation alone (9)

US: Search for Vitamin D in the Fullscript catalog.
CAN: Search for Vitamin D in the Fullscript catalog.

New and upcoming research

Cordyceps sinensis

Like many medicinal mushrooms, Cordyceps sinensis has a long history of use in traditional medicines, particularly Chinese and Tibetan medicines. (22) An entomopathogenic fungus, C. sinensis grows on the larva of insects in North America, Asia, Europe, and parts of India. (26) Unfortunately, its yield has decreased more than 90% in the last 25 years, making it increasingly rare and expensive. (10)

Numerous therapeutic benefits have been attributed to the biological activity of C. sinensis and its primary constituent, Cordycepin. It is thought to possess antioxidant, anti-inflammatory, antimicrobial, antitumor, immunomodulatory, hypoglycemic, anti-fatigue, hepatoprotective, and renal protective effects. C. sinensis may also enhance sexual and reproductive function. (10)(26)

Research findings:

  • Preliminary research shows that Cordyceps sinensis may balance the proportion between helper T cells and cytotoxic T cells (6)
  • In addition, Cordyceps sinensis may contribute to a significant decrease in anti-TPO antibodies in Hashimoto’s thyroiditis patients (6)

US: Search for Cordyceps sinensis in the Fullscript catalog.
CAN: Search for Cordyceps sinensis in the Fullscript catalog.

Cordyceps sinensis extract

C. sinensis grows on the larva of insects in North America, Asia, Europe, and parts of India.


Cannabis sativa L., commonly referred to as marijuana, (16) is a herbaceous plant that has been used recreationally and medicinally for over 5,000 years. While the use of cannabis has traditionally been controversial, acceptance of the plant as a therapeutic approach for certain health conditions continues to grow. (1)

The medicinal effects of cannabis have thus far been attributed to phytocannabinoids, or plant cannabinoids, which interact with cannabinoid receptors, CB1 and CB2, within the endocannabinoid system (ECS). (21) Found within the body’s central and peripheral nervous systems, the ECS is a lipid signaling system that plays an important role in regulating many body functions and maintaining homeostasis. (3) A recent study found that marijuana use may be associated with beneficial effects on thyroid function and autoimmunity.

Research findings:

  • It has been shown that recent marijuana users (used within the past 30 days), have lower TSH and anti-thyroperoxidase antibodies levels (11)

Key takeaways

While the cause of Hashimoto’s thyroiditis remains to be determined, research has demonstrated the beneficial effects of certain nutrients and plants, including selenium, vitamin D, Cordyceps sinensis, and cannabis. A protocol using natural supplements can be used therapeutically on its own or as an adjunct to existing treatment. If you are not an integrative healthcare provider, we recommend speaking with one to learn whether these supplements are right for your wellness plan.

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The Fullscript Integrative Medical Advisory team has developed or collected these protocols from practitioners and supplier partners to help health care practitioners make decisions when building treatment plans. By adding this protocol to your Fullscript template library, you understand and accept that the recommendations in the protocol are for initial guidance and may not be appropriate for every patient.

  1. Bridgeman, M. B., & Abazia, D. T. (2017). Medicinal cannabis: History, pharmacology, and implications for the acute care setting. Pharmacy and Therapeutics, 42(3), 180-188.
  2. de Farias, C.R., Cardoso, B.R., de Oliveira, G.M., de Mello Guazzelli, I.C., Catarino, R.M., Chammas, M.C., … Knobel, M. (2015). A randomized-controlled, double-blind study of the impact of selenium supplementation on thyroid autoimmunity and inflammation with focus on the GPx1 genotypes. Journal of Endocrinological Investigation, 38(10), 1065-74
  3. de Fonseca, F.R., del Arco, I., Bermudez-Silva, F.J., Bilbao, A., Cippitelli, A., & Navarro, M. (2005). The endocannabinoid system: Physiology and pharmacology. Alcohol and Alcoholism, 40(1), 2-14.
  4. Genetics Home Reference. (2019). Hashimoto thyroiditis. Retrieved from
  5. Gois, P., Ferreira, D., Olenski, S., & Seguro, A. C. (2017). Vitamin D and infectious diseases: Simple bystander or contributing factor?. Nutrients, 9(7), 651.
  6. He, T., Zhao, R., Lu, Y., Li, W., Hou, X., Sun, Y., … Chen, L. (2016). Dual-directional immunomodulatory effects of corbrin capsule on autoimmune thyroid diseases. Evidence-Based Complementary and Alternative Medicine: eCAM, 2016, 1360386.
  7. Hennessey, J., & Wartofsky, L. (2007). Hashimoto’s disease. The Journal of Clinical Endocrinology & Metabolism, 92(7), E1.
  8. Krysiak, R., Szkróbka, W., & Okopień, B. (2017). The effect of vitamin D on thyroid autoimmunity in levothyroxine-treated women with Hashimoto’s thyroiditis and normal vitamin D status. Experimental and Clinical Endocrinology & Diabetes, 25(4), 229-233.
  9. Krysiak, R., Szkróbka, W., & Okopień, B. (2018). Moderate-dose simvastatin therapy potentiates the effect of vitamin D on thyroid autoimmunity in levothyroxine-treated women with Hashimoto’s thyroiditis and vitamin D insufficiency. Pharmacological Reports, 70(1), 93-97.
  10. Lin, B., & Li, S. (2011). Cordyceps as an Herbal Drug. In I.F.F. Benzie, & S. Wachtel-Galor (Eds). Herbal Medicine: Biomolecular and Clinical Aspects (2nd edition). Retrieved from
  11. Malhotra, S., Heptulla, R.A., Homel, P., & Motaghedi, R. (2017). Effect of marijuana use on thyroid function and autoimmunity. Thyroid, 27(2), 167-173.
  12. Mazokopakis, E.E., Papadakis, J.A., Papadomanolaki, M.G., Batistakis, A.G., Giannakopoulos, T.G., Protopapadakis, E.E., & Ganotakis, E.S. (2007). Effects of 12 months treatment with L-selenomethionine on serum anti-TPO levels in patients with Hashimoto’s thyroiditis. Thyroid, 17(7), 609-12.
  13. Mazokopakis, E.E., Papadomanolaki, M.G., Tsekouras, K.C., Evangelopoulos, A.D., Kotsiris, D.A., & Tzortzinis, A.A. (2015). Is vitamin D related to pathogenesis and treatment of Hashimoto’s thyroiditis?. Hellenic Journal of Nuclear Medicine, 18(3), 222-7.
  14. Mincer, D.L., & Jialal, I. (2019). Hashimoto thyroiditis. In StatPearls. Retrieved from
  15. Nair, R., & Maseeh, A. (2012). Vitamin D: The “sunshine” vitamin. Journal of Pharmacology & Pharmacotherapeutics, 3(2), 118-126.
  16. National Center for Complementary and Integrative Health. (2018). Marijuana and cannabinoids. Retrieved from
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  18. National Institutes of Health. (2019). Selenium. Retrieved from
  19. National Institutes of Health. (2019). Vitamin D. Retrieved from
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  21. Pagotto, U., Marsicano, G., Cota, D., Lutz, B., & Pasquali, R. (2006). The emerging role of the endocannabinoid system in endocrine regulation and energy balance. Endocrine Reviews, 27(1), 73-100.
  22. Panda, A. K., & Swain, K. C. (2011). Traditional uses and medicinal potential of Cordyceps sinensis of Sikkim. Journal of Ayurveda and Integrative Medicine, 2(1), 9-13.
  23. Pirola, I., Gandossi, E., Agosti, B., Delbarba, A., Cappelli, C. (2016). Selenium supplementation could restore euthyroidism in subclinical hypothyroid patients with autoimmune thyroiditis. Endokrynologia Polska, 67(6), 567-571.
  24. Prabhu, K.S., & Lei, G.X. (2016). Selenium. Advances in Nutrition, 7(2), 415-417.
  25. Pyzik, A., Grywalska, E., Matyjaszek-Matuszek, B., & Roliński, J. (2015). Immune disorders in Hashimoto’s thyroiditis: What do we know so far?. Journal of Immunology Research, 2015, 979167.
  26. Tuli, H. S., Sandhu, S. S., & Sharma, A. K. (2014). Pharmacological and therapeutic potential of Cordyceps with special reference to Cordycepin. 3 Biotech, 4(1), 1-12.
  27. Wang, J., Lv, S., Chen, G., Gao, C., He, J., Zhong, H., & Xu, Y. (2015). Meta-analysis of the association between vitamin D and autoimmune thyroid disease. Nutrients, 7(4), 2485-2498.
  28. Wichman, J., Winther, K.H., Bonnema, S.J., & Hegedüs, L. (2016). Selenium supplementation significantly reduces thyroid autoantibody levels in patients with chronic autoimmune thyroiditis: A systematic review and meta-analysis. Thyroid, 26(12), 1681-1692.
  29. Zaletel, K., & Gaberšček, S. (2011). Hashimoto’s thyroiditis: From genes to the disease. Current Genomics, 12(8), 576–588.
  30. Zhang, R., & Naughton, D. P. (2010). Vitamin D in health and disease: Current perspectives. Nutrition Journal, 9, 65.