The current evolution in the design of fuel cell systems, together with the considerable development of integrated control techniques in microprocessor systems allows the development of portable fuel cell applications in which optimized control of the fuel cells performance is possible. Control, in the strict sense, implies a thorough knowledge of both the static and dynamic behaviour of the system comprising the stack, manifold and the compressor that enables oxygen supply. The objective of this control, far from being simply to maintain the stack free from oxygen and hydrogen shortages, is to achieve the necessary values of these gases, minimizing compressor consumption, which is the cause of the greatest inefficiency of fuel cells. This objective is essential when fuel cell systems are involved in situations where the net power of the stack is reduced and any unnecessary consumption lowers the total power available to the user. The design of an efficient control system requires the following steps: (1) modeling of the stack, compressor and other pneumatic elements involved in the system. (2) Calculation of the control equations and simulation of the entire system (including control). (3) Emulation of the stack and other pneumatic elements and simulation utilizing the designed control system. (4) Physical realization of the control system and testing within the fuel cell system. The design of a control system for fuel cell systems is introduced to manage PEMFC stacks. The control system will guarantee the correct performance of the stack around its optimal operation point, in which the net power is maximized. This means that both, the air flow and the stack temperature are controlled to a correct value. (C) 2007 Elsevier B.V. All rights reserved.