In the diurnal rodent Arvicanthis niloticus (grass rats) the pattern of expression of the clock genes and their proteins in the suprachiasmatic nucleus (SCN) is very similar to that seen in nocturnal rodents. Rhythms in clock gene expression have been also documented in several forebrain regions outside the SCN in nocturnal Ratus norvegicus (lab rats). To investigate the neural basis for differences in the circadian systems of diurnal and nocturnal mammals, we examined PER1 expression in the oval nucleus of the bed nucleus of the stria terminalis (BNST-OV), and in the basolateral (BLA) and the central (CEA) amygdala of male grass rats kept in a 12:12 light/dark cycle. In the BNST-OV, peak levels of PER1 expression were seen early in the light phase of the cycle, 12h out of phase with what has been reported for nocturnal lab rats. In the BLA the pattern of PER1 expression featured sustained high levels during the day and low levels at night. PER1 expression in the CEA was also at its highest early in the light phase, but the effect of sampling time was not statistically significant (p<0.06). The results are consistent with the hypothesis that differences between nocturnal and diurnal species are due to differences in neural systems downstream from the SCN.