The acyl-CoA dehydrogenases are a family of related enzymes which catalyze the alpha,beta-dehydrogenation of acyl-CoA esters, transferring electrons to electron-transferring flavoprotein. A cDNA for human short/branched chain acyl-CoA dehydrogenase has recently been cloned, and it has been suggested that this enzyme represents the human homolog for the previously reported 2-methyl branched chain acyl-CoA dehydrogenase purified from rat liver. We now report the cloning and expression of rat short/branched chain acyl-CoA dehydrogenase and characterization of its substrate specificity. The rat enzyme is more active toward longer carbon side chains than its human counterpart, while the human enzyme can utilize substrates with longer primary carbon chains. In addition, short/branched chain acyl-CoA dehydrogenase can utilize valproyl-CoA as a substrate. Northern blotting of mRNA shows ubiquitous tissue expression of both the rat and human enzyme. Further study of these enzymes will be helpful in understanding structure/function relationships in this gene family.