Ground squirrels undergo extreme body temperature fluctuations during hibernation. The effect of low body temperatures on the mammalian circadian system is still under debate. Using implanted temperature loggers, we recorded body temperature patterns in European ground squirrels kept in an enclosure under natural conditions. Although hibernation onset was delayed, hibernation end corresponded closely to that measured in a field population. Circadian body temperature fluctuations were not detected during deep torpor, but indications of circadian timing of arousal episodes at higher temperatures were found at the beginning and end of hibernation. One male exhibited synchronised arousals to a relatively constant phase of the day throughout hibernation. All animals first entered torpor in the afternoon. Daily body temperature fluctuations were decreased or distorted during the first days after hibernation. We hypothesise that hibernation may affect the circadian system by either decreasing the expression of the circadian oscillator, or by decreasing the amplitude of the circadian oscillator itself. possibly due to gradual, temperature dependent, internal desynchronisation. The latter mechanism may be beneficial because it might facilitate post-hibernation re-entrainment rates.