Daily torpor in the Djungarian hamster (Phodopus sungorus) is a precisely timed event gated by the circadian clock situated in the suprachiasmatic nuclei (SCN) of the hypothalamus. Timing-controlled hypothermia during which body temperature (Tb) decreases to ∼15 °C implies temperature compensation of the circadian system. Nevertheless, it remains controversial how the molecular clockwork functions at those low Tb values and whether the torpor bout affects the circadian system. In this study, we investigated rhythmic clock and clock-related gene as well as protein expression in the SCN and pineal gland of torpid and normothermic Djungarian hamsters over a 48 h cycle. We clearly demonstrate rhythmic gene expression of Per1, Bmal1 and Avp in the SCN as well as Aa-nat in the pineal gland on a day of torpor. Alterations in the phase and amplitude of these rhythms, however, may be due to decreased protein synthesis during hypothermia. This decreased protein feedback resulting from the hypothermia might also be responsible for changes in gene expression observed 1 day after a torpor bout. We conclude that temperature has at least a modulatory effect on the circadian system.