The fuel cell system and fuel cell gas turbine hybrid system represent an emerging technology for power generation because of its higher energy conversion efficiency, extremely low environmental pollution, and potential use of some renewable energy sources as fuels. Depending upon the type and size of applications, from domestic heating to industrial cogeneration, there are different types of fuel cell technologies to be employed. The fuel cells considered in this paper are mainly the molten carbonate (MCFC) and the solid oxide (SOFC) fuel cells, while a brief overview is provided about the proton exchange membrane (PEMFC). In all these systems, heat exchangers play an important and critical role in the thermal management of the fuel cell itself and the boundary components, such as the fuel reformer (when methane or natural gas is used), the air preheating, and the fuel cell cooling. In this paper, the impact of heat exchangers on the performance of SOFC, MCFC gas turbine hybrid systems and PEMFC systems is investigated. Several options in terms of cycle layout and heat exchanger technology are discussed from the on-design, off-design and control perspectives. A general overview of the main issues related to heat exchangers performance, cost and durability is presented and the most promising configurations identified.