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Polymer electrolyte and solid oxide are the two fuel cell types (PEFC, SOFC) under development in Switzerland. The very distinct operating temperatures of 80 °C (PEFC) and 800–950 °C (SOFC) impose fundamentally different requirements upon the nature of the fuel; normally purified H2 for the former (CO trace) and usually synthesis gas for the latter (H2, CO as main constituents). Apart from stored hydrogen, the most relevant fuels are primary hydrocarbons (natural gas, biogas, liquids,…), that then need processing (chemical conversion, cleaning) up to a level compatible with the fuel cell catalysts. These processes are briefly reviewed. Fuel compositions with an emphasis on impurities are given. Two application examples from Swiss R&D are presented: gasoline conversion to high purity H2 for PEFC and contaminated biogas processing for SOFC.