Expression profiles of rPer1 and rPer2 messenger RNAs, rat homologues of the Drosophila clock gene period, were examined in the rat suprachiasmatic nucleus, a main locus of circadian oscillation, with special reference to the topographical compartmentation of the suprachiasmatic nucleus. Quantitative in situ hybridization of rPer1 and rPer2 messenger RNAs showed a robust circadian rhythm in the suprachiasmatic nucleus, with a characteristic peak/trough profile in each gene: the peak of rPer1 messenger RNA was in the daytime and that of rPer2 messenger RNA was at the transition time of day to night in both light-dark and constant dark conditions. Light exposure at circadian time 16 increased both rPer1 and rPer2 messenger RNAs in the suprachiasmatic nucleus. In a detailed histological analysis, we found that light exposure at circadian time 16 induced the expression of rPer1 and rPer2 genes in neurons limited to the ventrolateral part of the suprachiasmatic nucleus, although the usual circadian rPer1 and rPer2 messenger RNA oscillation in light-dark and constant dark conditions occurred strongly in neurons in the dorsomedial part but weakly in neurons in the ventrolateral part of the suprachiasmatic nucleus. These rPer expression profiles indicate that the two major subpopulations of neurons in the suprachiasmatic nucleus play different roles in the generation of circadian rhythm: a strong autonomous expression ability with no light response in dorsomedial neurons and a strong light responsiveness with a weak autonomous expression in ventrolateral neurons.