Described herein are fuel cell systems and methods of using fuel cell systems. The systems include a fuel cell that generates electrical energy using hydrogen and a fuel processor that produces hydrogen from a fuel source. The fuel processor includes a reformer and a burner that heats the reformer. One heat efficient fuel cell system described herein heats internal portions of a fuel cell using a heating medium from a fuel processor. The heating medium may comprise gases exhausted at high temperatures from the fuel processor, which are then transported to the fuel cell. The heating medium may also include a gas that reacts catalytically in the fuel cell to produce heat. Systems and methods for expediting fuel cell system start up are provided. Methods for shutting down a fuel cell system are also described that reduce the amount of moisture and gases in the reformer and in one or more fuel cell components. One hydrogen efficient fuel cell system described herein transports hydrogen to an inlet of a burner. The hydrogen may comprise unused hydrogen from a fuel cell and/or hydrogen produced in a reformer. The burner comprises a catalyst that facilitates production of heat in the presence of the hydrogen.