It is thought that circadian regulation of physiology and behavior imparts survival advantages to organisms that use clocks. In mammals, a master clock resident in the SCN synchronizes other central and peripheral oscillators to evoke this regulation. This master oscillator consists of interlocking transcriptional-translational feedback loops, and it regulates both core clock genes necessary for oscillator maintenance as well as specific output genes that directly or indirectly mediate physiology under circadian control. It is now clear that both neuroanatomic and molecular outputs of the clock are necessary for proper circadian clock function. Recent technology has improved our understanding of these processes, elucidating the anatomic outputs of the SCN, as well as the molecular outputs of both central and peripheral oscillators that mediate observed physiological changes.