The Hormone That Helps Heartburn: Melatonin

Date: October 1, 2011      Publication: Bottom Line Natural Healing      Source: Mark A. Stengler      Print:

We tend to think of melatonin, often called the “sleep hormone,” in terms of—you guessed it—sleep. So what does melatonin have to do with your digestion? The answer is a lot. It turns out that this hormone, in addition to regulating our sleep/wake cycle, also can help gastroesophageal reflux disease (GERD). This is very good news! Melatonin is helping many GERD patients—and it may help you, too. For details, our editors turned to Mark Stengler, NMD, a naturopathic medical doctor and founder and medical director of the Stengler Center for Integrative Medicine in Encinitas, California, who explains how he uses melatonin for GERD.


Known for its symptoms of acid reflux or heartburn, GERD is a very common condition that occurs when the lower esophageal sphincter—the valve between the esophagus and the stomach—relaxes at the wrong time, allowing gastric acid to escape from the stomach into the esophagus. The result is pain and a burning sensation in the chest and throat. Over time, the acid exposure from GERD can damage the esophagus, even causing cancer and other serious conditions.

Using melatonin for GERD is important because there are so many problems with popular medications for GERD—namely, proton-pump inhibitors (PPIs) and H2 receptor antagonists, which work by suppressing stomach acid production. These drugs can cause health problems, particularly when used for an extended time. PPIs such as esomeprazole (Nexium) and omeprazole (Prilosec) have been linked to increased risk for hip, wrist and spine fractures (because they interfere with calcium absorption), diarrhea and pneumonia. H2 receptor antagonists such as ranitidine (Zantac) and cimetidine (Tagamet) also are associated with a range of unpleasant side effects, including headache, dizziness, fatigue, rashes, diarrhea and constipation. One study even suggests that their long-term use may increase risk for cognitive decline.


Melatonin is a naturally occurring hormone that is made in various parts of the body. When produced by the brain’s pineal gland (which happens whenever you’re exposed to darkness), melatonin has a strong influence on circadian rhythms and encourages sleep. It also has many other beneficial effects. Preliminary studies show that it is an effective treatment for migraine, obesity and seasonal affective disorder.

What many people don’t know: The gastrointestinal (GI) tract secretes up to 500 times as much melatonin as the pineal gland. Researchers have determined that the hormone plays an important role in the GI system by preventing oxidative stress on GI cells…regulating cholesterol uptake by the intestinal wall…helping to heal damage to the lining of the GI tract…and promoting the secretion of other hormones that aid digestion and elimination. Studies have shown that supplementing with melatonin can help to treat esophageal ulcers, dyspepsia (upset stomach) and irritable bowel syndrome.

But there also is evidence that melatonin supplements also alleviate GERD symptoms. One possible reason: Melatonin has been found to reduce gastric acid secretion (although not to the degree of PPIs) and to normalize pressure of the lower esophageal sphincter, allowing it to close more effectively.

In one study, published in Journal of Pineal Research, GERD patients received a daily supplement of 6 milligrams (mg) of melatonin, along with L-tryptophan, vitamin B-6, folic acid, vitamin B-12, methionine and betaine (the additional nutrients were administered for their anti-inflammatory and analgesic effects). An equal number of subjects were treated with daily 20-mg doses of the PPI omeprazole. Remarkably, after 40 days, 100% of the melatonin group reported no noticeable GERD symptoms, compared with just 65% of the omeprazole group.


Dr. Stengler recommends that patients with GERD take melatonin daily, about 30 minutes before bedtime. (Since his patients are already taking steps to reduce inflammation through diet and supplements, he does not have them take all the nutrients used in the study mentioned above.) He recommends the sublingual form for those who have trouble falling asleep or the time-release form if they tend to wake up during the night. Since every patient is different, it’s important that you check with your own holistic or naturopathic doctor about the dosage and form of melatonin that’s right for you. Melatonin is not recommended for children or for women who are pregnant.

Source: Mark A. Stengler, NMD, founder and medical director, Stengler Center for Integrative Medicine, Encinitas, California, author of the Health Revelations newsletter and The Natural Physician's Healing Therapies (Bottom Line Books).

  • alsports2000

    We know we are suppose to take melatonin before bedtime but what if you get heartburn in the middle of the day?

    • Neil

      For immediate relief take 1tbs of Bi-Carb Soda mixed with 2tbs of Apple Cider Vinegar. Mix in glass, wait for gas/bubbles to stop, mix with a little water and drink. This will save your life, naturally. Long term – Melatonin

      • Sherina

        Can you take melatonin with your acid reflux medication? I just started some and now I am just reading about melatonin

        • Mark M

          I read on another site that melatonin works well when taken with omeprazole. Omeprazole inhibits the acid and allows melatonin to go to work repairing the stomach lining and sphincter etc. Melatonin is the better long term option as it has other benefits as well whereas omeprazole may affect bone density and reportedly could harden your arteries.

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