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This paper presents the application of a new methodology for Fault Detection and Isolation (FDI) to a Fuel Cell System. The work is devoted to find an optimal set of sensors for model-based FDI. The novelty is that binary integer linear programming (BILP) is used in the optimization formulation, leading to a reformulation of the detectability and isolability specifications as linear inequality constraints. The approach has been successfully applied to a Fuel Cell System.