The circadian timing system is a neural network consisting of the hypothalamic suprachiasmatic nucleus, aided by the retina, other hypothalamic nuclei, autonomic regions of the spinal cord, sympathetic ganglia and the pineal gland. Extensive studies conducted over the last two decades have unravelled the principal items of its functional neuroanatomy. The system is responsible for the generation of the circadian rhythm, its synchronization by environmental factors such as light, and its mediation with respect to morphological, physiological and biochemical parameters of mammals that exhibit distinct alterations throughout the 24-h cycle. This review characterizes the brain sites involved and the pathways responsible for the generation and maintenance of circadian rhythmicity.