Circadian timing affects almost all life's processes. It not only dictates when we sleep, but also keeps every cell and tissue working under a tight temporal regimen. The daily variations of physiology and behavior are controlled by a highly complex system comprising of a master circadian clock in the suprachiasmatic nuclei (SCN) of the hypothalamus, extra-SCN cerebral clocks, and peripheral oscillators. Here are presented similarities and differences in the molecular mechanisms of the clock machinery between the primary SCN clock and extra-SCN brain clocks. Diversity of secondary clocks in the brain, their specific sensitivities to time-giving cues, as their differential coupling to the master SCN clock, may allow more plasticity in the ability of the circadian timing system to integrate a wide range of temporal information. Furthermore, it raises the possibility that pathophysiological alterations of internal timing that are deleterious for health may result from internal desynchronization within the network of cerebral clocks.