In-gel activity assays are useful tools to identify and characterize enzymes within gels. Prerequisite are electrophoretic protein separations that are carried out under conditions compatible with enzyme activity. While blue native-polyacrylamide gel electrophoresis (BN-PAGE) is widely used for activity assays of the five enzyme complexes of the oxidative phosphorylation system, the blue background of this electrophoretic system is not compatible with activity assays for some other mitochondrial enzymes. As an alternative system, clear native (CN)-PAGE can be used for visualizing activities of mitochondrial enzymes. Here, we describe enzyme activity assays for mitochondrial enzymes in BN and CN gels.