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In transportation research programs, two types of fuel cells are under primary consideration for application in heavy-duty vehicles: Phosphoric acid (PAFC) and proton exchange membrane (PEM). The following discussion will include the main differences between the phosphoric acid and proton exchange membrane fuel cells and explain the differences between their applications in transportation research. A central focus of this paper will be the application of PAFC technology in a 40 foot transit bus program with which TMC is currently associated, and a discussion of the PEM technology and its potential for heavy-duty transit applications. Included will be a discussion of the fuels which can potentially be used with fuel cells such as methanol, natural gas, ethanol, hydrogen, and finally, an overview of technical challenges related to the fuel cell.