The up-regulation of heart- and adipose-type fatty acid binding proteins (H-FABPs and A-FABPs) was detected during hibernation in brown adipose tissue (BAT) of 13-lined ground squirrels, Spermophilus tridecemlineatus, using a commercial rat cDNA array. Full length cDNAs encoding H-FABPs and A-FABPs were subsequently retrieved from a BAT cDNA library. These cDNAs were used to probe Northern blots of total RNA from tissues of euthermic versus hibernating ground squirrels. H-FABP mRNA transcripts increased in BAT, skeletal muscle and heart of hibernating animals whereas A-FABP transcripts, which are normally expressed exclusively in adipose tissue, increased in both BAT and heart during torpor. It is proposed that the increased expression of H-FABPs and A-FABPs during hibernation accelerates the rate at which fatty acids can be transported to the mitochondria for oxidization, particularly in support of the huge increase in thermogenesis by BAT and rapid increase in heart rate that are required during arousal from torpor. Comparison of the deduced polypeptide sequence of ground squirrel H-FABP with that from other mammals also revealed three unique amino acid differences which may be important for protein function at low body temperatures during hibernation.