Rare earth (or yttriurn) doped BaCeO3 has been widely investigated as a proton conducting material. Usually, the trivalent dopants are assumed to occupy the Cell-site, which introduces oxygen vacancies into the perovskite structure and furthers the protonic conductivity. Recent studies indicate the possibility of dopant incorporation on the Ba2+-site, which is unfavorable for protonic conductivity. In this work atomistic simulation techniques, especially the supercell approach, have been developed to investigate the questions of dopant site-selectivity and cation nonstoichiometry in doped BaCeO3. Our calculations predict that, on eneractic grounds, Ba2+- C, site deficiency shifts trivalent dopant incorporation onto the Ba2(+)-site. These results confirm that the dopant partitioning or site-occupancy of trivalent dopants will be sensitive to the precise Ba/Ce ratio. and hence to the experimental processing conditions. The relative energies explain the experimentally observed "amphoteric" behavior of Nd with significant dopant partitioning over both Ba and Cc sites. Such partitioning reduces the concentration of oxygen vacancies, which, in turn, lowers proton uptake and decreases proton conductivity relative to dopant incorporation solely on the Ce4+-site.