Circadian rhythms play an important role in many physiological processes. We have previously reported that no periodic fluctuation in the Bmal1 mRNA is observed in the liver of the chipmunk, a mammalian hibernator, in the hibernation season, suggesting that peripheral circadian clocks are not functional during hibernation. In contrast, the Per2 mRNA levels are transiently increased by elevated body temperature during interbout arousal and showed periodic fluctuations in the hibernation season, suggesting that periodic expression of the Per2 mRNA may be restored during interbout arousal. In the present study, we analyzed Per1 gene expression in the chipmunk liver. The Per1 mRNA showed circadian fluctuations with a peak during the late sleep period in the non-hibernation season and periodic fluctuations with a peak during the early interbout arousal in the hibernation season. In both the non-hibernation and hibernation seasons, Per1 gene expression was phase-advanced relative to Per2 gene expression, and the phase relationship between the two genes was maintained, suggesting that for some genes, periodic gene expression, similar to circadian expression in the non-hibernation season, may be restored during interbout arousal. Interestingly, Per1 gene transcription was differentially activated by BMAL1 in the non-hibernation season and possibly by CREB1 in the hibernation season.