Proton exchange membrane (PEM) fuel cells experience performance degradation, such as reduction in efficiency and life, as a result of poisoning of platinum catalysts by airborne contaminants. Research on these contaminant effects suggests that the best possible solution to allowing fuel cells to operate in contaminated environments is by filtration of the harmful contaminants from the cathode air. A cathode air filter design methodology was created that connects properties of cathode air stream, filter design options, and filter footprint, to a set of adsorptive filter parameters that must be optimized to efficiently operate the fuel cell. Filter optimization requires a study of the trade off between two causal factors of power loss: first, a reduction in power production due to poisoning of the platinum catalyst by chemical contaminants and second, an increase in power requirements to operate the air compressor with a larger pressure drop from additional contaminant filtration. The design methodology was successfully applied to a 1.2kW fuel cell using a programmable algorithm and predictions were made about the relationships between inlet concentration, breakthrough time, filter design, pressure drop, and compressor power requirements.