Expression of the immediate-early genes (IEGs) c-fos and junB in the rat brain was studied in response to sleep deprivation (SD) starting at four time points during the light phase of a 12:12 light:dark cycle. Animals were confined to slowly rotating wheels for 3 or 6 h in order to prevent sleep. The numbers of c-Fos- and JunB-immunoreactive cells were assessed in seven brain regions previously reported to respond to SD with increased c-fos expression (medial preoptic area (MPA), cortex, anterior and posterior paraventricular thalamic nuclei, amygdala, caudate-putamen, and laterodorsal tegmental nucleus). While c-Fos was induced by SD in all regions studied, there were differences in levels of induction depending on the duration of deprivation and on the timing of the deprivation period during the light phase. The most robust induction occurred in most regions in response to 3-h deprivation periods beginning 3 h into the light phase. A similarly timed peak of induction was observed in the MPA and cortex after 6 h of SD. In two regions, the posterior paraventricular thalamic nucleus and amygdala, 6 h of deprivation induced greater c-Fos immunoreactivity than did 3 h of deprivation, collapsed across all phases tested. Increased JunB immunoreactivity in response to either duration of deprivation was more limited and was significant only in the MPA, cortex, caudate-putamen and amygdala. c-Fos and JunB immunoreactivity in the paraventricular hypothalamic nucleus was low and similar in control and deprived animals. These results indicate that both duration of prior wakefulness and time of day influence the extent of IEG expression differentially in brain regions responsive to SD. The results also suggest that the posterior paraventricular thalamic nucleus and amygdala might be primarily responsive to length of wakefulness (sleep drive), while the MPA and anterior paraventricular thalamic nucleus might integrate input related to both homeostatic sleep drive and circadian clock influences on sleep regulation.