Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, an epigenetic clock model is proposed that outlines how molecular modifications, such as DNA methylation, are an integral component for endogenous biological rhythms. The model provides a novel framework for the environmental and hormonal regulation of endogenous epigenetic oscillations. The hypothesis proposed is that the epigenetic clock model serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells: from unicellular to complex organisms.