Melatonin is associated with few side effects. However, morning grogginess, undesired drowsiness, sleepwalking, and disorientation have been reported. Researchers have hypothesized that certain people should not use melatonin supplements, including pregnant or breast-feeding women, people with depression or schizophrenia, and those with auto-immune disease, including lupus, at least until more is known.^{9, 10}

In one study, administration of 3 mg per day of melatonin for three months resulted in a marked decline in sperm counts and a decline in sperm quality in two of eight healthy young men.¹¹ In one of these two men, sperm count and quality became normal after melatonin was discontinued. Although this was a small study, it raises the possibility that long-term use of melatonin could lead to infertility.

In a group of children suffering from neurological disorders, 1–5 mg of melatonin per night led to an increase in the rate of seizures despite the fact that sleep improved.¹² Until more is known, children with neurological conditions should take melatonin only under medical supervision.

Many other side effects have been attributed to melatonin supplementation, including inhibition of sex drive, severe headaches, abdominal cramps, and formation of rudimentary breasts in men.^{13, 14} However, these associations have not been supported by solid evidence.^{15, 16, 17, 18} Since none of these claims have been well documented or independently confirmed, these problems may not have been due to melatonin.

Though most research reports that melatonin improves the quality of sleep, at least one trial has found that four of fifteen men given melatonin had their sleep patterns disturbed by supplemental melatonin.¹⁹

One case of painful gynecomastia (enlarged breasts) has been reported involving a 56-year-old man who had been suffering from amyotrophic lateral sclerosis (Lou Gehrig’s disease), and was taking 1–2 mg melatonin per day for one and a half years.²⁰ As the signs and symptoms disappeared after melatonin was discontinued, the authors of the report suspected that melatonin caused this side effect.

According to a preliminary report, blood levels of melatonin may be elevated in women with fibromyalgia.²¹ Data in this report did not indicate toxicity from melatonin, nor did the report suggest that melatonin causes or exacerbates the symptoms of fibromyalgia. It did suggest there is no current rationale for melatonin supplementation in people with fibromyalgia.

One-time oral administration of 1 mg of melatonin to post-menopausal women reduced glucose tolerance and insulin sensitivity when tested 45 minutes after administration.²² This finding suggests that people with diabetes should use melatonin with caution and only under the supervision of a doctor.