A promising application for high temperature polymer electrolyte fuel cells (HT-PEFC) is the use in auxiliary power units (APU). In combination with a fuel gas processor for middle distillates like kerosene or diesel it can efficiently provide on board electric energy for mobile applications. Current R&D work focuses on robust, long-term stable and efficient operation of HT-PEFC stacks. In order to gain insight into internal electrical and thermal behavior current density and temperature distribution measurements in a five cell short stack have been performed. With this method it is shown, how reactant supply and temperature management impacts on local polarization characteristics and temperature distribution.