The fuel cell technology is an emerging technology for electric power generation for stationary, mobile and portable applications. While tremendous technological progress has been made in the last 10 years, it is going to take another 10 years for commercialization and considerable penetration of power generation by fuel cell systems. The most promising fuel cell types are proton exchange membrane (PEMFC), molten carbonate (MCFC) and solid oxide fuel cells (SOFC) while the phosphoric acid fuel cells (PAFC) are commercially available for up to about 200 kW units. Direct methanol fuel cells (DMFC) are considered for portable power applications such as electronic devices. After a brief discussion of these fuel cell systems, the major challenges and research opportunities are outlined for automotive, stationary and portable power generation applications. This includes electrocatalysis, water and thermal management, modeling, and other challenges. The focus is on the R & D needs for each of these fuel cells starting at the cell level, followed by stack level, system level including combined gas turbine and cogeneration systems as well as fuel processing.