Melatonin, an indoleamine neurohormone that is synthesized mainly in the pineal gland and derived from 5-HT, has many effects on a wide range of physio-pathological functions. Some of these effects are mediated by the interactions of melatonin with the two melatonin MT1 and MT2 receptors. Other effects are often suggested to be due to the chemical antioxidant nature of this indoleamine, and are observed at high, non-physiological concentrations. However, it is increasingly believed that some of these effects are due to interactions with other protein targets. In this review, we summarize the molecular pharmacology of melatonin, including the main enzymes involved in its synthesis and catabolism, and the proteins that mediate its actions. Furthermore, various compounds, mainly inhibitors and antagonists, that can be used to dissect these functions and pathways are presented.