Sleep is consistently concentrated to a specific time of the day. Its timing and consolidation depend on the interplay between a homeostatic and a circadian process of sleep regulation [1-3]. Sleep propensity rises as a homeostatic response to increasing wake time, whereas a circadian clock determines the specific time when sleep will probably occur. This two-process regulation of sleep also determines which specific sleep stage will be manifested, and the circadian process governs tightly the manifestation of rapid eye movement sleep (REMS) [1, 4]. The role of the hypothalamic suprachiasmatic nucleus (SCN) in the circadian gating of sleep and wakefulness has been unequivocally established by lesion studies [5], but its role in the timing of specific sleep stages has remained unknown. Using a forced desynchrony paradigm that induces the stable dissociation of the ventrolateral (vl) and dorsomedial (dm) SCN, and a jetlag paradigm that induces desynchronization between these SCN subregions, we show that the SCN can time the occurrence of specific sleep stages. Specifically, the circadian regulation of REMS is associated with clock gene expression within the dmSCN. We provide the first neurophysiological model for the disruption of sleep architecture that may result from temporal challenges such as rotational-shift work and jetlag.