In constant dim illumination the hamster estrous cycle free-runs with a period that is a quadruple multiple of the concurrently recorded rhythm of wheel-running activity; both activity and estrous cycles are generated by biological clocks. Maintenance of stable phase angle differences between heat onset and running onset before and after treatment with deuterium oxide suggests that a common circadian system generates periodicities in estrus and activity. An organization of the estrous cycle is proposed in which the stimulus for the ovulatory surge of luteinizing hormone is generated by a circadian system that includes the suprachiasmatic nuclei of the hypothalamus. Various possible interactions of estradiol and photoperiod with the neurogenic stimulus for the luteinizing hormone surge are described and implications of different types of circadian organization of the estrous cycle for theories of sexual differentiation are considered.