The structure of sleep across the night as expressed by the hypnogram, is characterised by repeated transitions between the different states of vigilance: wake, light and deep non-rapid eye movement (NREM) sleep, and rapid eye movement (REM) sleep. This review is concerned with current knowledge on these state transitions, focusing primarily on those findings that allow the integration of data at cellular level with spectral time-course data at the encephalographic (EEG) level. At the cellular level it has been proposed that, under the influence of circadian and homeostatic factors, transitions between wake and sleep may be determined by mutually inhibitory interaction between sleep-active neurons in the hypothalamic preoptic area and wake-active neurons in multiple arousal centres. These two fundamentally different behavioural states are separated by the sleep onset and the sleep inertia periods each characterised by gradual changes in which neither true wake nor true sleep patterns are present. The results of sequential spectral analysis of EEG data on moves towards and away from deep sleep are related to findings at the cellular level on the generating mechanisms giving rise to the various NREM oscillatory modes under the neuromodulatory control of brainstem-thalamic activating systems. And there is substantial evidence at cellular level that transition to and from REM sleep is governed by the reciprocal interaction between cholinergic REM-on neurons and aminergic REM-off neurons located in the brainstem. Similarity between the time-course of the REM-on neuronal activity and that of EEG power in the high beta range (18–30Hz) allows a tentative parallelism to be drawn between the two. This review emphasises the importance of the thalamically projecting brainstem activating systems in the orchestration of the transitions that give rise to state progression across the sleep–wake cycle.