Ultra-low sulphur diesel (ULSD) is the preferred fuel for mobile auxiliary power units (APU). The commercial available technologies in the kW-range are combustion engine based gensets, achieving system efficiencies about 20%. Solid oxide fuel cells (SOFC) promise improvements with respect to efficiency and emission, particularly for the low power range. Fuel processing methods i.e., catalytic partial oxidation, autothermal reforming and steam reforming have been demonstrated to operate on diesel with various sulphur contents. The choice of fuel processing method strongly affects the SOFC's system efficiency and power density. This paper investigates the impact of fuel processing methods on the economical potential in SOFC APUs, taking variable and capital cost into account. Autonomous concepts without any external water supply are compared with anode recycle configurations. The cost of electricity is very sensitive on the choice of the O/C ratio and the temperature conditions of the fuel processor. A sensitivity analysis is applied to identify the most cost effective concept for different economic boundary conditions. The favourite concepts are discussed with respect to technical challenges and requirements operating in the presence of sulphur. Crown Copyright (C) 2010 Published by Elsevier B.V. All rights reserved.