Fuel Cells (FC) are most relevant elements for the increase of efficiency of energy conversion processes and hence contribute in the improvement of the global climate situation. Whereas the development of fuel cells for passenger car applications has intensified during the last years, commercial vehicle applications have not been in the focus of developers as much. A reason for that is the limited availability of hydrogen for PEM fuel cells as well as the fact that commercial vehicles are operated with diesel fuel. AVL has developed a modular approach for stand-alone and highly integrated SOFC APUs (Solid Oxide Fuel Cell Auxiliary Power Unit) for commercial vehicles operated with regular diesel fuel. Based on integrational studies, two APU concepts were investigated: a Stand-Alone-System' for an early market entry and a highly integrated option (AVL PTSU - 'Power Train Support Unit') for efficient support of the main power train. The assembled system consisted of a 1kW SOFC Stack (from Topsoe Fuel Cell), a prereformer, a heat exchanger and a catalytic afterburner. Via the HiL (Hardware in the Loop) interface, a DC/DC converter and the air compressor models have been coupled to the hardware assembly. The two major tasks of the controller are the power management and the thermal management of the stack.The operating point of the fuel cell stack is controlled such that the requested effective power as well as power for auxiliaries (e.g. air compressor) are both available. The power controller monitors the safe operation of all individual cells of the stack through the AVL developed THDA monitoring system. Consequently, without extensive individual cell voltage measurements, the controller recognizes critical operational states and, hence, can react and correct in time.