Fuel cells (FCs) offer significant environmental benefits over competing technologies and hence the environment is a strong driving force behind the development of FC systems for transport and stationary applications. This paper provides a comprehensive comparison of FC and competing systems, and points out strengths and weaknesses of the different FC systems, suggesting areas for improvement. The results presented build on earlier work [D, Hart, G. Hormandinger, Initial assessment of the environmental characteristics of fuel cells and competing technologies, ETSU F/02/00111/REP/1, ETSU, Harwell, UK, 1997.] and provide a detailed analysis of a wider range of systems. The analysis takes the form. of a model, which compares system emissions (global, regional and local pollutants) and energy consumption on a full fuel cycle basis. It considers a variety of primary energy sources, intermediate fuel supply steps and FC systems for transport and stationary end-uses. These are compared with alternative systems for transport and stationary applications. Energy and pollutant emission reductions of FC systems compared to alternative vehicle technology vary considerably, though all FC technologies show reductions in energy use and CO2 emissions of at least 20%, as well as reductions of several orders of magnitude in regulated pollutants compared to the base-case vehicle. The location of emissions is also of importance, with most emissions in the case of FC vehicles occurring in the fuel supply stage. The energy, CO2 and regulated emissions advantages of FC systems for distributed and baseload electricity are more consistent than for transport applications, with reductions in regulated pollutants generally larger than one order of magnitude compared to competing technologies. For CHP applications, the advantages of FC systems with regard to regulated pollutants remain large. However, energy and CO2 emission advantages are reduced, depending largely on the assumptions made for the heat/power ratio and system comparison.