3-Hydroxyacyl-CoA epimerase is a peroxisomal enzyme and therefore not involved in mitochondrial fatty acid oxidation.

The subcellular location of 3-hydroxyacyl-CoA epimerase (EC 5.1.2.3) was studied by differential centrifugation and Percoll density gradient centrifugation of a rat liver homogenate. The enzyme was found to be associated with peroxisomes but not with mitochondria. This observation proves that 3-hydroxy-acyl-CoA epimerase does not function in mitochondrial beta-oxidation of polyunsaturated fatty acids which are degraded by a modified pathway.