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A simulation of a “fuel cell engine” (FCE) based on a proton exchange membrane (PEM) fuel-cell stack was developed using a process simulation software package. Rates of emissions of unburned methanol, formaldehyde, CO and NOx were calculated based on chemical equilibria. The predicted rates of emissions for unburned methanol, formaldehyde and CO were found to all be less than 1 μg/km. This is considerably less than has been reported in the literature but represents a theoretical limit which should be achievable as effective catalytic-combustion systems are developed for hydrogen/methanol fueled burners. The worst-case rate of NOx emissions was shown to be less than 0.03 g/km (0.05 g/mi.). It was found that increasing the rate of heat transfer in the steam reformer, which converts the methanol to a hydrogen-rich gas, significantly reduced the rate of NOx emission due to the lower burner temperatures which could be used.