The circadian timing system provides a temporal structure across an organism to modulate and synchronize biological function. The mammalian circadian system is composed of many individual clocks. Circadian clocks are found in individual cells that have to be synchronized by a central pacemaker. This pacemaker can be viewed as a managing director who coordinates temporal physiology and behavior in the organism. In this review I will discuss the current understanding of the clock mechanism at the molecular level, how it adjusts to environmental changes and what the implications of a defect in the circadian clock are on mammalian physiology.