The theoretically calculated dimerization-induced shifts of the lowest excitation energies in two model systems, adenine−thymine and guanine−cytosine base pairs, are analyzed. The applied formalism is based on first principles and allows one to study the influence of the microscopic environment of a given molecule on its ground- [Wesolowski, T. A.; Warshel, A. J. Phys. Chem. 1993, 97, 8050] and excited-state [Casida, M. E.; Wesolowski, T. A. Int. J. Quantum Chem. 2004, 96, 577] properties. The assessment of the relative importance of such effects as (a) Coulomb interactions, (b) orbital interactions, (c) electronic polarization of the environment, and (d) electron density overlap effects is straightforward in this formalism. In the applied formalism, electron density overlap effects can be further decomposed into the exchange−correlation component which provides a small attractive contribution and the repulsive kinetic energy-dependent component. It is shown that the shifts can be attributed to the electrostatic interactions and the repulsive overlap-dependent term in the embedding potential. The electronic polarization of the environment plays a significant role (up to 30% of the total shift) only in transitions involving the orbitals localized on hydrogen bond donor groups. For all analyzed shifts, the contribution of the intermolecular orbital interactions is negligible. The analysis of this work provides strong evidence supporting the use of the widely applied embedding-molecule strategy in computational studies of chromophores in a condensed phase even in such cases where only one end of the hydrogen bond is included in the quantum mechanical part.