Circadian rhythm refers to the inherent 24-h cycle oscillation of biochemical, physiological and behavioral functions, which is almost universal in eukaryotes. At least 14 core clock genes have been reported to form multiple chain feedback loops that confer intrinsic circadian rhythmicity onto the molecular clock. Accumulating evidence has shown that the circadian gene dysfunction resulted from single nucleotide polymorphisms (SNPs), deletions, epigenetic modification, and deregulation is strongly associated with cancer risk. In the present review, we describe the composition of circadian rhythm system. We highlight the function and mechanism of clock genes in cancer pathogenesis and progression. Moreover, their potential clinical implications as prognostic biomarkers and therapeutic targets have been addressed.