In SOFCs, the most common separator materials are oxide ion conductors, in particular YSZ, requiring operation temperatures of more than 800 degrees C. However, several oxides are known to incorporate significant amounts of water at low temperatures and high water partial pressures. Thus protonic defects are generated and proton conductivity exceeding that of oxygen ions can be achieved in this temperature range. In this contribution, we discuss some of the material constraints for the application of perovskite-type proton conductors as separator material in SOFC fuel cells. At this stage thermodynamic stability data may be obtained from experiments only while both experiments and quantum molecular dynamics simulations provide mobility parameters. The calculated results for the model systems ABO(3) (A = Sr, Ba; B = Zr, Ce) are in reasonable agreement with experimental single crystal data. This provides some confidence into the predictive power of the simulation technique. The calculations may also be used as a tool to support the development of new proton conducting oxides in particular with respect to applications as separator material in SOFC fuel cells.