The fuel cell system is an emerging technology for power generation because of its higher energy conversion efficiency and extremely low environmental pollution. Depending upon the applications, there are several types of fuel cell systems used for stationary, mobile and portable power generation. The most common types of fuel cells considered are the proton exchange membrane (PEMFC), direct methanol (DMFC), phosphoric acid (PAFC), molten carbonate (MCFC) and solid oxide (SOFC) fuel cells. These fuel cells use hydrogen as the fuel. If a hydrocarbon fuel is used, the fuel needs to be reformed to make it hydrogen rich or almost pure hydrogen depending upon the operating temperature and the type of the fuel cell. Heat exchangers play an important and critical role in the fuel cell systems to reform the fuel, to preheat the fuel and oxidant to the cell/stack operating temperature, to humidify the incoming fuel and oxidant streams, to recover water and energy, to cool the fuel cell stack and incoming high pressure air and reformed hydrogen, and in general, to control thermal management of the fuel cell systems. In this paper, heat exchangers used in various fuel cell systems are discussed along with their design philosophy and operating environment.