Fuel cells and electrolysers have the potential for supplying three main energy services to the end-users: electricity, heat and transport; and can replace existing less efficient or more polluting technologies. The challenge is to identify in which applications these technologies should be used for. In the future energy systems, the key technologies are intermittent energy resources, such as wind turbines, solar photovoltaics, solar thermal and wave power, as well as more efficient energy conversion technologies, such as CHP and energy savings in demand. In the thesis, different applications of fuel cells and electrolysers in future energy systems have been analyzed.