H-Bonded and stacked structures of the cytosine dimer were studied at the MP2/6-31G* ab initio level. In addition, the electrostatic energy was estimated separately using correlated distributed multipole analysis (CDMA) with atomic multipoles calculated at the MP2/6-31G* level. The H-bonded structure is more stable; the stabilization of the optimal stacked structure is, however, quite large and constitutes almost 50% of the H-bonded pair stabilization. The dominant part of the H-bonded stabilization originates in the electrostatic interaction. The dispersion energy is responsible for the stabilization in the stacked pair, while the mutual orientation of the stacked cytosines is governed by the electrostatic term. Due to the dipole-dipole interactions, antiparallel arrangement of the two stacked cytosines in the isolated cytosine dimer is strongly favored. No significant stabilization originating in the interactions between the polar exocyclic groups and the delocalized electrons of the aromatic rings was found. The CDMA calculations gave good insight into the nature of the stabilization of various complexes; however, some regions of the potential energy surface were not satisfactorily reproduced by this method.