Energy conversion today is subject to high thermodynamic losses. About 50% to 90% of the exergy of primary fuels is lost during conversion into power or heat. The fast increasing world energy demand makes a further increase of conversion efficiencies inevitable. The substantial thermodynamic losses (exergy losses of 20% to 30%) of thermal fuel conversion will limit future improvements of power plant efficiencies. Electrochemical conversion of fuel enables fuel conversion with minimum losses. Various fuel cell systems have been investigated at the Delft University of Technology during the past 20 years. It appeared that exergy analyses can be very helpful in understanding the extent and causes of thermodynamic losses in fuel cell systems. More than 50% of the losses in high temperature fuel cell (molten carbonate fuel cell and solid oxide fuel cell) systems can be caused by heat transfer. Therefore system optimization must focus on reducing the need for heat transfer as well as improving the conditions for the unavoidable heat transfer. Various options for reducing the need for heat transfer are discussed in this paper. High temperature fuel cells, eventually integrated into gas turbine processes, can replace the combustion process in future power plants. High temperature fuel cells will be necessary to obtain conversion efficiencies up to 80% in the case of large scale electricity production in the future. The introduction of fuel cells is considered to be a first step in the integration of electrochemical conversion in future energy conversion systems.