The calculation of quantum similarity measures from second-order density functions contracted to intracule and extracule densities obtained at the HartreeFock level is presented and applied to a series of atoms, (He, Li, Be, and Ne), isoelectronic molecules C 2 H 2 , HCN, CNH, CO, and N 2 ), and model hydrogen-transfer processes (H 2 aH , H 2 aH á , H 2 aH À ). Second-order quantum similarity measures and indices are found to be suitable measures for quantitatively analyzing electronpair density reorganizations in atoms, molecules, and chemical processes. For the molecular series, a comparative analysis between the topology of pairwise similarity functions as computed from one-electron, intracule, and extracule densities is carried out and the assignment of each particular local similarity maximum to a molecular alignment discussed. In the comparative study of the three hydrogen-transfer reactions considered, secondorder quantum similarity indices are found to be more sensitive than ®rst-order indices for analyzing the electron-density reorganization between the reactant complex and the transition state, thus providing additional insights for a better understanding of the mechanistic aspects of each process.