Abstract A rigorous method for partitioning the molecular interaction energy into classical electrostatic, charge-transfer, and wavefunction relaxation contributions is proposed. The energy components, defined with quantities central to density functional theory, are calculated with the help of the topological theory of atoms in molecules. Since the new scheme does not rely on Hilbert space partitioning, it is applicable to any level of electronic structure theory and it yields energy components that are true observables converging smoothly at the limit of a complete basis set. For this reason, the new method does not possess the deficiencies of the previously introduced Morokuma-Kitaura and Glendening-Streitwieser approaches. The results of several test calculations are compared with those obtained with the other energy partitioning schemes and found to exhibit superior numerical stability with respect to the quality of basis sets.