Melatonin in itself is known to cause very few side-effects in the short term. When taken as pills externally for up to 3 months, healthy people do not show side effects. Melatonin is generally safe within recommended doses. However, since melatonin pills are several thousand times stronger than body’s own melatonin production there may be some of the side effects of melatonin preparations.

Some of these include:

• Some studies have shown reduction of body temperature.
• There may be sluggish blood flow on long term use.
• Melatonin can cause somnolence (drowsiness). This is important for persons operating heavy machinery or driving. Patients on melatonin should be cautioned against driving or operating heavy machinery
• Melatonin has a dubious role in immunity. In patients who have autoimmune disorders, melatonin supplementation may either exacerbate or reduce symptoms due to immunomodulation. The interactions with immunity are unpredictable.
• Patients who develop orthostatic hypotension tend to worsen with melatonin. Orthostatic hypotension means sudden fall in blood pressure when a person stands up and there is pooling of blood in the lower limbs. Melatonin supplements tend to worsen this condition. By reducing nerve activity the situation is worsened with melatonin.
• If melatonin from animal pineal gland is used as supplements, there is a risk of transmission of viral infections from the animal to humans. This risk is eliminated if the synthetic version of the melatonin molecule is used.
• There have been a few reports on psychomotor disturbances. This includes disorientation, fatigue, headache, dizziness, etc.
• Some people tend to be more at risk of seizures.
• Melatonin alone or in combination with other drugs may also raise the risk of blood clotting abnormalities. This may lead to hematuria or blood in urine.
• There might be some hormonal interactions. Thus pregnant and breast feeding women need to consult their doctors before taking melatonin.
• There may be some gastrointestinal side effects like diarrhea
• Some patients may be more prone to urinary tract infections