Mammalian hibernation is an adaptive strategy to conserve energy during periods of low food availability in highly seasonal or unpredictable environments. During hibernation, when mammals undergo long periods of physical inactivity, reduced mechanical load on the skeleton may lead to the muscle atrophy as it is shown in non-hibernating mammals. However, hibernating mammals demonstrate unique ability to preserve muscle mass and strength over prolonged periods of immobility and starvation. We conducted comparative analysis of transcriptional changes in the skeleton muscle during hibernation and summer activity in two mammal species which demonstrate different hibernation patterns – the black bear (BB) and the arctic ground squirrel (AGS). Experiments with custom cDNA microarrays revealed that among 2,138 genes presented on both BB and AGS microarrays, 56 genes were differentially expressed in both species. The Gene Ontology analysis showed that during hibernation, the categories of protein biosynthesis and ribosomal biogenesis were significantly enriched by over expressed genes. Oxidation reduction genes demonstrated a tendency for down regulation in hibernating animals. Elevated expression of protein biosynthesis genes suggests induction of translation that may be related to common for both species adaptive mechanisms reducing muscle atrophies over extended periods of low metabolism and immobility during hibernation.