Circadian oscillators orchestrate daily rhythms in behaviour and physiology to adapt to the predictable daily appearance of light. Identifying the complement of circadian-regulated transcripts in major organs is critical in the understanding of both the biochemical targets of clock regulation and the mechanism of such control. Recent analysis of temporal gene expression patterns in peripheral and central oscillators have revealed hundreds of circadian-regulated transcripts, most of which are tissue-specific. Mapping of these transcripts to physiological processes and pathways has revealed that major functions of those organs tested are under circadian regulation, and importantly, key and rate-limiting steps in these processes are often the targets of circadian control. Overall, nearly 100% of the mammalian genome may be regulated by the clock, demonstrating the pervasive control of the circadian oscillator in temporal coordination of transcription throughout the organism. This wealth of circadian outputs offers exciting challenges to deciphering systems-level transcriptional regulatory mechanisms that underlie spatiotemporal gene expression.