Negative feedback loops regulating clock genes such as Per2, Baml1 and cryptochromes (Cry1, Cry2) constitute the molecular basis of endogeneous oscillations with a period of about 24 h. About 20,000 synchronized neurons in the suprachiasmatic nucleus (SCN) control daily rhythms of physiology, metabolism, and behaviour. We show that mathematical modelling contributes to an understanding of the complex temporal organization at the levels of single cells, the synchronization of neurons, and the entrainment of organismic rhythms.