Expression patterns of mammalian clock genes, Clock and BMAL1, were examined by in situ hybridization in the pineal body, olfactory bulb, hippocampus and cerebellum in rats under constant darkness. In the pineal, the level of Clock transcript was significantly higher at ZT18 (subjective night) than at ZT6 (subjective day), while the level of BMAL1 transcript was significantly higher at ZT6 than at ZT18. A 30 min light pulse did not affect the transcript levels of Clock nor of BMAL1. The Clock expression in the cerebellum was significantly increased at ZT6 than at ZT18, while no difference was detected in the olfactory bulb and hippocampus at these two phases. The BMAL1 expressions in these areas were similar to the case in the pineal. These findings indicate that the mammalian clock gene, Clock and BMAL1, are expressed differently in the different areas of the brain and the pineal.