3-Phenylpropionic acid is an end-product of the bacterial degradation of unabsorbed phenylalanine in the intestinal lumen. As CoA ester, this metabolite has been considered to be a specific substrate for medium chain acyl-CoA dehydrogenase (MCAD). Its glycine-conjugate, 3-phenylpropionylglycine, has now been established as a pathognomonic marker in urine from patients affected with MCAD deficiency. However, no systematic studies to evaluate the reactivity of 3-phenylpropionyl-CoA with other known acyl-CoA dehydrogenases have so far been carried out to establish the specificity of this substrate for MCAD. We studied the in vitro reactivity of 3-phenylpropionyl-CoA with five rat and human liver acyl-CoA dehydrogenases using purified preparations. we demonstrated that MCAD effectively dehydrogenated 3-phenylpropionyl-CoA, and that no other acyl-CoA dehydrogenase exhibited any significant activity with this substrate. In the steady state condition, the Km of 3-phenylpropionyl-CoA for human MCAD was 50 microM. Gas chromatography/mass spectrometry analysis of the assay mixture identified trans-cinnamoyl-CoA as the product of the reaction. Furthermore, we showed by determination of the reaction products using gas chromatography/mass spectrometry selected ion monitoring that, in absence of the primary electron acceptor, 3-phenylpropionyl-CoA was slowly but significantly dehydrogenated by MCAD under aerobic conditions. These data suggest that MCAD may oxidize 3-phenylpropionyl-CoA in vivo using an alternative electron acceptor, to produce trans-cinnamoyl-CoA. This mechanism provides an explanation for the normal 3-phenylpropionylglycine excretion observed in urine from patients affected with glutaric aciduria type II and ethylmalonic/adipic aciduria.