Atmospheric carbon dioxide and pollution due to the burning of fossil fuels is increasing. Many scientists attribute global warming to the rising levels of carbon dioxide and other pollutants, some of which also pose risks to health. These can be reduced by the more efficient use of conventional fuels and the development of non-polluting energy resources. Fuel cells offer a highly efficient and low polluting method of generating electricity, and are under development for both the power generation and transport sectors. There is a need to assess (a) emissions from fuel cells using various fuels and (b) ways of introducing such technology to transportation in the near future. Fuel consumption, energy and emissions from the production and use of fuels (hydrogen, methane, propane, petrol, diesel, alcohols and rape methyl ester) are calculated per kilowatt hour of fuel cell output over a range of efficiency. These are compared with those for internal combustion engines with advanced exhaust control and for the recharging of battery driven vehicles. The results, which are applicable to both transport and power generation, enable the best low pollution fuels to be selected and are used to calculate through life emissions for public transport buses. Fuel cells are an ideal solution to reduce pollution from transport, but their commercial development in this field is further away than that for stationary applications. Thus, a transition stage is recommended where fuel cell electrical power stations, based on existing demonstrators, are used to recharge fleets of battery driven vehicles during the development of mobile fuel cell systems. These fleets include public transport and commercial vehicles. Also, fuel cell power stations could provide energy for electric trains. A combined system is proposed where electric trains recharge battery driven commercial vehicles during long journeys. The above proposals would enhance fuel cell development, introducing them alongside current transport systems, possibly using the same fuel.