Exogenous melatonin is widely used in humans for multiple pharmacologic purposes. The metabolic pathways of melatonin reflect the fate and functions of melatonin in vivo. This study was designed to re-profile melatonin metabolism in humans using a metabolomic approach. In the urine of healthy subjects treated with 10 mg melatonin, sulfate- or glucuronide-conjugated metabolites of melatonin were detected, including 6-hydroxymelatonin sulfate, 6-hydroxymelatonin glucuronide, N-acetylserotonin glucuronide, N-acetylserotonin sulfate, and an unknown sulfated metabolite (X). The molecular weight of metabolite X was 14 Da smaller than 6-hydroxymelatonin sulfate, but 16 Da larger than N-acetylserotonin sulfate. Further studies suggest that metabolite X was produced via O-demethylation, 6-hydroxylation, and sulfation. The antioxidant products of melatonin, N(1)-acetyl-N(2)-formyl-5-methoxykynuramine and N(1)-acetyl-5-methoxy-kynuramine, were not detected in human urine. In summary, this study provided a global view of melatonin metabolism in humans and extended our knowledge of enzyme-dependent pathways of melatonin metabolism.