Mesoscale convective systems (MCSs) can bring up to 60% of summer rainfall to the central United States but are not simulated by most global climate models. In this study, a new empirical orthogonal function based index is developed to isolate the MCS activity, similar to that developed by Wheeler and Hendon (2004) for the Madden-Julian Oscillation. The index is applied to compactly compare three conventional- and super-parameterized (SP) versions (3.0, 3.5, and 5.0) of the National Center for Atmospheric Research Community Atmosphere Model (CAM). Results show that nocturnal, eastward propagating convection is a robust effect of super-parameterization but is sensitive to its specific implementation. MCS composites based on the index show that in SP-CAM3.5, convective MCS anomalies are unrealistically large scale and concentrated, while surface precipitation is too weak. These aspects of the MCS signal are improved in the latest version (SP-CAM5.0), which uses high-order microphysics.