Melatonin and the thyroid

Skeletal formula: Lukáš Mižoch. Design: BOOST Thyroid.

Skeletal formula: Lukáš Mižoch. Design: BOOST Thyroid.

The impact of melatonin on Hashimoto’s and autoimmunity

Melatonin (aka the darkness hormone) plays a major role in your well-being. It helps you to have a balanced sleep-wake cycle and it’s been marketed as a medicine that can fix lots of problems, like severe headaches. 

Melatonin has a direct impact on thyroid function, as well as on several autoimmune diseases. However, a lot of things remain unclear about melatonin’s connection to Hashimoto’s, as research has been conflicting and limited. 

What is melatonin?

Melatonin helps the body maintain its circadian rhythm, your internal 24-hour “clock”. It’s produced by the pineal gland—a tiny gland near the center of your brain. Melatonin can also be taken as a medication or supplement.

If you live under normal conditions of lightness and darkness, your body will produce melatonin at night. It has a cyclical nature, it starts rising between 6PM and 8PM and peaks between midnight and 5AM (1-5). Melatonin’s main function is to transfer information about your circadian rhythm to your body’s cells and organs. This helps with timing the functions of cells—such as regulating your core body temperature, blood sugar, hormone production, immune system, and sleep-wake cycle.

Melatonin levels are highest during childhood, between 2 and 4 years old. Levels then decrease and plateau during puberty. From puberty, there is a steady decline as you age with a more rapid decrease starting in your early 50s (6-12). This follows a similar pattern of thyroid function decline as you age.

Disruption of melatonin production can be a sign of high stress or illness—and vice versa. All of this can lead to more severe symptoms and/or impair the success of disease management and treatment (13- 15).

What is the difference in function between melatonin produced by your body and medical melatonin in the form of a pill? 

More research is needed here. Studies thus far have only focused on some aspects (i.e. dose but not duration of effects).

Impact of melatonin on the thyroid gland

Research to date has focused mostly on one specific function of melatonin in regards to impact on thyroid gland function—melatonin as an antioxidant (like vitamin C). Antioxidants remove potentially damaging reactive oxygen species (ROS) from your cells and organs.

ROS are very important for everyday cell functioning. They trigger oxidative reactions in your cells in all tissues and organs. However in excess, ROS cause oxidative damage to molecules in your cells, which makes them dysfunctional. In the thyroid gland, ROS are necessary to complete the synthesis of thyroid hormones.

Some research shows that specialized cells (C-cells) found in the thyroid gland are capable of producing of melatonin. This happens under thyroid stimulating hormone (TSH) control, a similar process to how T4 is made. It seems that melatonin and TSH balance themselves out (16).

Melatonin can block thyroid cell proliferation and thyroid hormone synthesis. If you’re supplementing with melatonin medication for prolonged periods of time you should check your thyroid hormone levels (17-19-6).

Impact of melatonin on the immune system and its role in autoimmunity

Your immune system function is greatly affected by melatonin. It interacts with many (if not all) immune system cells—activating and suppressing certain functions.

Melatonin suppresses molecules that promote inflammation and regulates the immune system in a dose-dependant way. It functions differently by dose amount when taken as a medication, which can be 10 or 100x higher than the levels produced by a healthy body.

From protecting against inflammation, melatonin also regulates the immune system in your gut. By doing this it possibly reduces the immune reaction in the entire body. Research discovered this in ulcerative colitis (UC), a chronic inflammatory disease of the colon (20).

Effects of melatonin in autoimmune conditions (17, 20):

  • Multiple sclerosis (MS) — MS deregulates melatonin production, while treatment with melatonin blocks the onset of the flare-ups.

  • Rheumatoid arthritis (RA) — melatonin has a disease-promoting effect in RA, and its impact is also influenced by your biological sex.

  • Type 1 diabetes — melatonin can be beneficial as it stimulates insulin production.

  • Irritable bowel syndrome (IBS) — melatonin reduces flare-ups in intensity and duration.

Jet-lag, melatonin, and your thyroid

Jet-lag is insomnia or excessive daytime sleepiness associated with transmeridian (east–west or west–east) flight travel across at least two time zones. Sometimes it can cause problems, like difficulty with normal daily functioning, general weakness, and digestive trouble (21).

Issues from the mismatch between the sleep-wake cycle of a person and the day-night time in the environment can be even more pronounced in people with thyroid disorders. TSH and T3 production in your body is dependent on your sleep-wake cycle, but also on natural light cycles (22). TSH levels change according to changes in sleep patterns (23)—so night shift work changes levels of thyroid, insulin, and sex hormones, and can increase the risk of autoimmune diseases (24-26).

Melatonin can help decrease jet-lag when taken close to your desired bedtime, with daily doses of between 0.5 and 5mg considered effective (26).

How to measure melatonin?

Melatonin produced by your body is usually measured in biochemical clinical labs. There are several different protocols—measured through blood serum, saliva, and/or urine. Sometimes melatonin is measured directly, and sometimes its metabolites (byproducts) are measured. All of these measurements should be equally precise, even though most melatonin can be found in your blood (26).

Potential for Hashimoto’s

Research studies focusing on melatonin therapy in autoimmune diseases have been examined in many animal models and in a few human clinical trials. Melatonin has been shown to have the potential to reduce the severity of symptoms in most autoimmune conditions (except rheumatoid arthritis) (27).

These findings indicate that melatonin treatment could be an important strategy for Hashimoto’s. Unfortunately, research on this topic is lacking, especially as we are aware of melatonin’s potential dual role in thyroid function and in immune response.

As for opposing effects, research should dig deeper and address the following:

  • Which is more beneficial—blocking the autoimmune part of Hashimoto’s while tampering with thyroid hormone production, or the other way around?

  •  What’s the optimal effect and dosage for Hashimoto’s patients?

More research is needed to better understand the delicate balance between melatonin and thyroid gland function. People diagnosed with hypothyroidism disorder are generally advised to check their thyroid levels if they start regularly using melatonin. Hopefully in the near future there will be more research focused on understanding this connection.


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  12. Lahiri DK, et al. Melatonin, metals, and gene expression implications in aging and neurodegenerative disorders, 2004

  13. Claustrat B, et al. Melatonin: Physiological effects in humans, 2015

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  15. NIH. Circadian Rhythms Fact Sheet, 2017

  16. Garcia-Marin R, et al. Melatonin in the thyroid gland: regulation by thyroid-stimulating hormone and role in thyroglobulin gene expression, 2015

  17. D’Angelo G, et al. Atopy and autoimmune thyroid diseases: melatonin can be useful, 2016

  18. Karbownik M, et al. The role of oxidative stress in physiological and pathological processes in the thyroid gland; possible involvement in pineal-thyroid interactions, 2003

  19. Chojnacki C, et al. Evaluation of melatonin effectiveness in the adjuvant treatment of ulcerative colitis, 2011

  20. Thorpy MJ. Classification of sleep disorders, 2012

  21. Hirschfield U. Progressive elevation of plasma thyrotropin during adaptation to simulated jet lag: effects of treatment with bright light or zolpidem, 1996

  22. Patel YC, et al. The 24-hour plasma thyrotrophin profile, 1972

  23. Davis S, et al. Night shift work and hormone levels in women, 2012

  24. Holmbäck U, et al. Endocrine responses to nocturnal eating--possible implications for night work, 2003

  25. Boscolo P, et al. Environmental and occupational stress and autoimmunity, 2008

  26. Herxheimer A, et al. Melatonin for the prevention and treatment of jet lag, 2002

  27. Lin GJ, et al. Modulation by melatonin of the pathogenesis of inflammatory autoimmune diseases, 2013

Skeletal formula: Lukáš Mižoch. Design: BOOST Thyroid.