The NADPH-dependent reduction pathway for the metabolism of Delta(5)-unsaturated fatty acids involves the isomerization of trans-2,Delta(5)-dienoyl-CoA, initially formed from the dehydrogenation of Delta(5)-enoyl-CoA, to isomeric Delta(3),Delta(5)-dienoyl-CoA. The latter intermediates were then isomerized to trans-2,trans-4-dienoyl-CoA, which then follows the NADPH-dependent pathway mediated by 2,4-dienoyl-CoA reductase. The isomerization from trans-2,Delta(5)-dienoyl-CoA to Delta(3),Delta(5)-dienoyl-CoA is catalyzed by Delta(3),Delta(2)-enoyl-CoA isomerase. In this investigation, we identified the stereoisomers of Delta(3),Delta(5)-dienoates that were formed in the reaction. Starting from trans-2,cis-5-decadienoyl-CoA, the isomerization produced cis-3,cis-5- and trans-3,cis-5-decadienoates. On the other hand, trans-2,trans-5-decadienoyl-CoA yielded cis-3,trans-5- and trans-3,trans-5-decadienoates. In addition to purified rat liver Delta(3),Delta(2)-enoyl-CoA isomerase, acyl-CoA oxidase from Arthrobacter also catalyzed the isomerization from trans-2,cis-5-dienoyl-CoA. However, this acyl-CoA oxidase could not catalyze the similar isomerization of trans-2,trans-5-dienoyl-CoA. Delta(3),Delta(5)-t-2,t-4-Dienoyl-CoA isomerase used cis-3,cis-5-, trans-3,cis-5-, and cis-3,trans-5-dienoyl-CoA's as substrates and converted them to trans-2,trans-4-dienoyl-CoA. In contrast, trans-3,trans-5-dienoyl-CoA was not a substrate for this isomerization. Extensive purification of acyl-CoA oxidase through column chromatography could not remove or diminish the isomerization activity associated with acyl-CoA oxidase. Acyl-CoA oxidases derived from Candida and rat liver also possess isomerization activity. In contrast, acyl-CoA dehydrogenases from beef liver could not catalyze the isomerization. The dehydrogenation and isomerization of cis-5-enoyl-CoA's catalyzed by commercially available acyl-CoA oxidase preparations render the preparation of Delta(3),Delta(5)-dienoyl-CoA's feasible. The data obtained so far tend to rule out the possibility that the isomerase activity of acyl-CoA oxidase was due to contaminating enzymes.