We studied the impact of hibernation and food supply on relative telomere length (RTL), an indicator for aging and somatic maintenance, in free-living edible dormice. Small hibernators such as dormice have ∼50% higher maximum longevity than non-hibernators. Increased longevity could theoretically be due to prolonged torpor directly slowing cellular damage and RTL shortening. However, although mitosis is arrested in mammals at low body temperatures, recent evidence points to accelerated RTL shortening during periodic re-warming (arousal) from torpor. Therefore, we hypothesized that these arousals during hibernation should have a negative effect on RTL. Here, we show that RTL was shortened in all animals over the course of ∼1 year, during which dormice hibernated for 7.5-11.4 months. The rate of periodic arousals, rather than the time spent euthermic during the hibernation season, was the best predictor of RTL shortening. This finding points to negative effects on RTL of the transition from low torpor to high euthermic body temperature and metabolic rate during arousals, possibly because of increased oxidative stress. The animals were, however, able to elongate their telomeres during the active season, when food availability was increased by supplemental feeding in a year of low natural food abundance. We conclude that in addition to their energetic costs, periodic arousals also lead to accelerated cellular damage in terms of RTL shortening. Although dormice are able to counteract and even over-compensate for the negative effects of hibernation, restoration of RTL appears to be energetically costly.