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The performance of the fuel cells (FCs) are today very appealing for industrial, transportation and home power generation applications and their use is widely increased during recent years. Unfortunately, in dynamic conditions the FCs behavior can present some lacks of power, due to the transitions between two steady-state current levels. To better design these kind of applications, a FC model is required, to evaluate the performance at different working conditions. The synthesis of a dynamic model describing the FC behavior should be performed starting form the real system configuration, including pipes, flow and pressure regulators and valves. To this aim an automatic measurement system for the characterization of PEM (polymer electrolyte membrane) fuel cells has been developed, and in this paper a dynamic model of a fuel cells stack is proposed, which has been validated through experimental measures.