A cDNA library constructed from kidney of the thirteen-lined squirrel, Spermophilus tridecemlineatus, was differentially screened for genes that were upregulated during hibernation. A clone encoding cytochrome c oxidase subunit 1 was found and confirmed to have been upregulated by northern blotting. Differential expression of Cox1 mRNA occurred in multiple organs during hibernation; in hibernating animals transcript levels were twofold higher in kidney and fourfold higher in heart and brown adipose tissue than in euthermic animals, but were unchanged in skeletal muscle. Transcript levels of mitochondrial-encoded ATP synthase 6/8 were similarly upregulated in these tissues whereas transcript levels of the nuclear encoded subunits Cox4 and ATP synthase alpha did not change during hibernation. Immunoblot analysis revealed a 2.4-fold increase in Cox 1 protein and a slight decrease in Cox 4 protein in kidney of hibernating squirrels, compared with euthermic controls. Hibernating mammals may increase the expression of the mitochondrial genome in general, and Cox1 specifically, to prevent or minimize the damage to the electron transport chain caused by the cold and ischemia experienced during a hibernation bout.