The suprachiasmatic nucleus (SCN) is the mammalian circadian pacemaker, which consists of thousands of oscillator cells. It is believed that the circadian oscillation in each cell is generated by the transcription/(post)-translation feedback loop of a set of clock genes. However, little is known about how these oscillator cells are organized to produce the robust circadian rhythms in the SCN. In the present study, we examined the expression of the clock genes Per1 and Per2 paying particular attention to the topographic compartmentalization of the SCN. In the rat SCN, the dorsomedial (SCNDM) and ventrolateral (SCNVL) compartments are clearly delineated by chemical characteristics of neurons and neuronal afferents. In the SCNDM, Per1 mRNA was initially expressed at the most dorsomedial region along the third ventricle (SCNDMPV, periventricular part of the dorsomedial compartment of the SCN) at CT0, and then spread laterally to the central dorsomedial region (SCNDMCe, central part of the dorsomedial compartment of the SCN), reaching peaks at subjective day and troughs at subjective night. In contrast, in the SCNVL, Per1 expression showed a weak, two-peak pattern in one circadian cycle. Per2 expression was also robust in the SCN, showing very similar circadian profiles among these three subdivisions with a slightly earlier phase in SCNDMPV than that in SCNDMCe. We also investigated the Per1 and Per2 expression in response to a light exposure at early subjective night. The light pulse induced both Per1 and Per2 expression, which was restricted in the SCNVL neurons. The present findings suggest that the phase and amplitude of the circadian expression of clock genes are not uniform, and there are topographic neuron groups that have different properties in the SCN.