Fuel Cell cars are a strategic part of research and development in the automotive industry, due to their high environmental compatibility and their high efficiency. Proton Exchange Membranes (PEM) are the most promising fuel cell technologies for transportation applications. PEM Fuel Cells are widely used for other applications either in industry or residential. Independently of the problems of integration and cost, the use of PEM Fuel Cell (PEMFC) in a vehicle requires to fully control its behavior and also all its ancillaries. Indeed, the power efficiency of the PEMFC system does not only depend on the stack but also on the response of the ancillaries that are located around the stack. In order to run the fuel cell in good conditions and to increase the lifetime of the fuel cell system, the whole control has to be carefully operated. In this article, a fuel cell system is described with its local and global controls. Diagnosis methods for fuel cell system are also presented.