In this work the effect of the basis set superposition error (BSSE) is explored with the counterpoise method oil the occupied and unoccupied Hartree-Fock (HF) and Kohn-Sham (KS) orbitals. Three different systems linked by hydrogen bonds. (H2OFH)-F-.... (H2OH2O)-H-..., and (H2OCFH3)-C-..., were studied by using the basis set families cc-pVXZ and aug-cc-pVXZ (X = D, T, Q). The basis sets were tested with the HF method and two approximations for the exchange-correlation functional of KS: a generalized gradient approximation and a hybrid approach. In addition to these methods, the second-order Moller-Plesset perturbation theory, MP2, was considered. It was found that the presence of the "ghost" basis set affects the orbitals in two ways: (1) The occupied KS orbitals are more sensitive to the presence of this "ghost" basis set than the occupied HF orbitals. For this reason the BSSE observed in HF is less than that obtained with KS. (2) The unoccupied HF orbitals are more sensitive to the presence of the "ghost" basis set than their corresponding occupied orbitals. Because the MP2 method uses both, occupied and unoccupied HF orbitals. to compute the total energy, the contribution of the BSSE is bigger than that obtained with HF or KS methodologies.