This paper describes recent applications of heat pipe technology in fuel cell systems, which include new stack designs with heat pipes to improve heat transfer as well as work on fuel cell system level design and engineering with adopting the heat pipe concept. In one design, micro-heat pipes are inserted and bonded in bipolar plates for thermal control in the fuel cell stack. In another design, flat heat pipes are integrated with a carbon bipolar plate for improving thermal control in the fuel cell stack. Finally, based on the heat pipe concept, we specifically developed a series of direct methanol fuel cell (DMFC) systems characterized as passive technology for methanol fuel delivery, water recirculation, and air and thermal management. Long-term durability and stability of the passive DMFC systems have been proved experimentally.