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Fuel cell systems appear as a good alternative for future power generation. This is mainly due to their high energy conversion efficiency and simple operation. Since the output of the fuel cell is low voltage DC, fuel cell systems supplying power to AC loads are usually constructed using a two stage approach cascading a DC-DC converter and an inverter. It can be shown that in such a system the current drawn from the fuel cell under normal single phase (or unbalanced three phase) operation contains a large second harmonic component. Due to the internal impedance of the fuel cell stack the presence of low frequency current ripple has as side effect additional heating, and more importantly, a reduction in its output power thus diminishing the power availability and power conversion efficiency of the system. To mitigate this problem an auxiliary power converter is proposed in this paper. The proposed converter operates as an active filter supplying the low frequency ripple current demanded by the power converter allowing the fuel cell stack to supply the DC component, which in turn optimizes system operation. In addition the proposed converter, if suited with an energy storage element such as a supercapacitor, can be controlled to supply transient load changes further improving stack characteristics.