We have recently shown that the expression of two immediate-early genes, c-fos and NGFI-A, is strongly affected by sleep deprivation, In this work, we investigated c-fos and NGFI-A expression after periods of spontaneous wakefulness or sleep. We used in situ hybridization and immunocytochemistry to detect the corresponding mRNA and protein levels, respectively. A first group of rats (S-L) was sacrificed during the light hours at the end of a long period of sleep. A second group (W-L) was sacrificed under similar conditions, except that during the last half hour the animals had been spontaneously awake. A third group (W-D) was sacrificed during the dark hours after a long period of continuous wakefulness. We found that c-fos and NGFI-A expression in several brain areas was increased in W-L and W-D rats with respect to S-L rats. Some of these areas, including the cerebral cortex, basal ganglia, and colliculi, may have been activated by the increased sensory and motor activity associated with waking. The activation of other areas, such as the medial preoptic area of the hypothalamus and some brainstem nuclei, may be more directly related to sleep regulation. These results indicate that many regions showing an increased expression of immediate early genes after wakefulness induced by sleep deprivation are also activated by periods of spontaneous wakefulness.