Hibernation consists of a series of physiological and biochemical alterations in an animal that allows for reduced body temperatures down to near ambient levels and substantial fuel conservation allowing it to survive on stored fat supplies accumulated during the summer. The Richardson's ground squirrel is one such hibernator that undergoes such changes for as long as 9 months of the year. This study examines the role of regulation of the pyruvate dehydrogenase complex (PDC) during hibernation in the skeletal muscle and liver of the Richardson's ground squirrel. The current study demonstrates a great reduction in the activity of PDC in the hibernating liver, but not in the skeletal muscle. This was matched by a significant increase in the phosphorylation on a regulatory serine residue (S300) of the pyruvate dehydrogenase (PDH) E1α subunit. Examining the expression patterns of the relevant kinases for PDH and the associated phosphatase demonstrated some unexpected results. Specifically, an increase in PDKs 1 and 2 and a decrease in PDK4 was noted in the skeletal muscle tissue in response to hibernation and no alterations in the expression patterns of any of these enzymes were noted in the liver. This suggests that alternative modes of regulation of the kinases may be at play in hibernation to bring about the observed effects. Taken together this study demonstrates that PDH regulatory responses differ markedly between tissues and emphasize the importance of inhibition of the complex in the liver during hibernation.