We performed a high temporal resolution analysis of the transcript level of two core clock genes, Period2 (Per2) and Bmal1, and a clock output gene, Dbp, in the suprachiasmatic nucleus (SCN), the master circadian clock, and in two forebrain regions, the lateral part of the central nucleus of the amygdala (CEAl), and dentate gyrus (DG), in rats. These regions, as we have shown previously, exhibit opposite rhythms in expression of the core clock protein, PERIOD2 (PER2). We found that the expression of Per2, Bmal1 and Dbp follow a diurnal rhythm in all three regions but the phase and amplitude of the rhythms of each gene vary across regions, revealing important regional differences in temporal dynamics underlying local daily rhythm generation in the mammalian forebrain. These findings underscore the complex temporal organization of subordinate circadian oscillators in the forebrain and raise interesting questions about the functional connection of these oscillators with the master SCN clock.