The conformation dependences of basis set superposition errors (BSSE) for 1,2-difluoroethane (DFE) and 1,2-dimethoxyethane (DME) molecules have been estimated using counterpoise method at the Moller-Plesset second order perturbation (MP2) level of theory with various basis sets, assuming that all BSSE dependences on conformations are due to the change in CC bond. The BSSE on the energy differences between eclipsed and gauche forms of DFE are in the range of 0.2-1.2 kcal/mol and those between local minima, gauche and anti forms, are less than 0.2 kcal/mol. For the larger DME molecule, the BSSE differences between local minima are still less than 0.4 kcal/mol, but may not be ignored compared to the energy differences of 0.2-3.0 kcal/mol between conformers.