The intermolecular interaction energies for hydrogen-bonded complexes have been investigated using density functional theory (DFT). Contributions to the exchange energy were estimated with the Slater-Dirac (S), Becke (B), and X alpha functionals. Exchange-correlation effects were estimated with the exchange functional of Becke and the correlation energy functional of Vosko, Wilk, and Nusair (B-VWN), the exchange functional of Becke and the correlation energy functional of Lee, Yang, and Parr (B-LYP), and the Slater-Dirac exchange and Lee Yang and Parr (S-LYP) and Vosko, Wilk, and Nusair correlation functionals (S-VWN). In addition, the hybrid method B3-LYP has been tested. The following complexes were fully optimized with the above functionals : HF-HF, H2O-H2O, C2H2-H2O, CH4-H2O, and NH3-NH3. All the optimizations were carried out with Pople’s split valence 6-31++G(2d,2p), basis set. For each of these complexes, interaction energies have been calculated using the correlation consistent polarized valence double-zeta (cc-pVDZ), Pople’s split valence (6-31++G(2d,2p) and augmented correlation consistent polarized valence triple-zeta (aug-cc-pVTZ) basis sets at the MPn (n = 2, 3, and 4) and DFT levels. The importance of the basis set superposition error (BSSE) is addressed for each density functional approximation and basis sets. DFT calculations with small basis sets (cc-pVDZ) are more sensitive to BSSE than MPn methods. The interaction energies of the HF-HF, H2O-H2O, C2H2-H2O, CH4-H2O and NH3-NH3 hydrogen-bonded complexes estimated with BS-LYP/6-31++G(2d,2p) are -4.68, -4.82, -2.65, -0.12, and -2.67 kcal/mol, respectively.