In mammals, the rhythmic secretion of melatonin from the pineal gland is driven by the circadian clock in the suprachiasmatic nucleus (SCN) of the hypothalamus. The robust nightly peak of melatonin secretion is an output signal of the circadian clock and is supposed to deliver the circadian message to the whole of the organism. Since the circadian system regulates many behavioral and physiological processes, its disruption by external (shift-work, jet-lag) or internal desynchronization (blindness, aging) causes many different health problems. Externally applied melatonin is used in humans as a chronobiotic drug to treat desynchronization and circadian disorders, and the success of these treatments does, at first glance, underline the supposed pivotal role of melatonin in the synchronization of the circadian system. On the other hand, pinealectomy in experimental animals and humans does not abolish their rhythms of rest and activity. Furthermore, mice with deficient melatoninergic systems neither display overt defects in their rhythmic behavior nor do they show obvious signs of disease susceptibility, let alone premature mortality. During the last years, our laboratory has investigated several mouse stains with intact or compromised internal melatonin signaling systems in order to better understand the physiological role of the melatoninergic system. These and other investigations which will be reviewed in the present contribution confirm the synchronizing effect of endogenous melatonin and the melatoninergic system. However, these effects are subtle. Thus melatonin does not appear as the master of internal synchronization, but as one component in a cocktail of synchronizing agents.