This study examined the effects of sleep deprivation on the expression of the immediate early gene c-fos in the brain with both in situ hybridization and immunocytochemistry. Rats were manually sleep-derived for 3 h, 6 h, 12 h, and 24 h starting at light onset (08.00 hours), and for 12 h starting at dark onset (20.00 hours). c-Fos expression was found to be higher in sleep-deprived rats with respect to control animals in several brain areas. The increase was evident both in terms of c-fos mRNA and Fos protein, although with a different time course. Among the areas that showed a consistent induction of c-fos were many cortical regions, the medial preoptic area and the posterior hypothalamic area, some thalamic nuclei, and several nuclei of the dorsal pontine tegmentum. The pattern of c-fos expression after sleep deprivation was very similar to that observed after comparable periods of spontaneous wakefulness (Pompeiano et al. 1994). In general, the increase in c-fos expression was not simply proportional to the amount of previous wakefulness. In many areas, the highest levels of c-fos were seen after 3 h of sleep deprivation. These observations are discussed with respect to the homeostatic regulation of sleep and to the functional consequences of wakefulness in specific brain areas.