The focus of this review is recent studies of the mammalian circadian pacemaker in the suprachiasmatic nucleus (SCN) of the hypothalamus. The anatomy of the SCN and its major afferents from the retina, raphe, and intergeniculate leaflet (IGL) of the thalamus are considered, with a special emphasis on the effects of afferent interaction on the circadian timekeeping system. What is known of the endogenous clock mechanism is reviewed in comparison with known molecular circadian mechanisms in other species. Efferents of the SCN are also discussed with a view toward understanding how circadian information is transmitted to the rest of the central nervous system. Where possible, anatomical, electrophysiological, neuropharmacological, molecular, and behavioral data are integrated in an attempt to illuminate the mechanisms of circadian timekeeping.