Global climate change is assumed to be a significant threat to biodiversity. The expected increase in average temperature will not only lead to an increase in extreme hot temperatures in summer, but also decrease the number of cold days in winter. A large fraction of temperate zone endotherms is undergoing winter hibernation and therefore are highly sensitive to changes in environmental temperature. Higher hibernation temperatures will increase the number of interbout arousals during hibernation and frequent arousals are expected to increased telomere shortening. We experimentally tested this hypothesis by comparing telomere dynamics and hibernation pattern of garden dormice (Eliomys quercinus), a fat-storing hibernator, hibernating at different temperatures with or without access to food. Garden dormice were allowed to hibernate during the winter month in climate chambers set to either 3°C or 14°C and we used recordings of nest temperature as a proxy for body temperature to estimate torpor use, frequency of rewarming from torpor and length of interbout euthermia. Further, we estimated telomere length by a quantitative PCR technique  using DNA extracted from the inner cheeks by gently twisting a small brushfor ca 30 s inside each cheek. Our results show that relative telomere length was positively affected by warmer winter temperature, even when no food was available. In contrast, hibernation at cold temperature led to a reduction in telomere length when animals had no access to food, while individuals were able to increase telomere length when food was available. Our data show that hibernation at low body temperatures comes with costs on a cellular level and that hibernators can actively counterbalance telomere shortening.