The world's energy consumption is growing extremely rapidly. Fuel cell systems are of interest by researchers and industry as the more efficient alternative to conventional thermal systems for power generation. The principle of fuel cell conversion does not involve thermal combustion and hence in theory fuel cell systems can be far more efficient than thermal power systems. This advantage is only partly utilized in present fuel cell pilot plants and additional optimization is needed. The complexity of fuel cell systems makes the optimization process anything but simple. This thesis presents the results of studies to understand the complex interactions between the different segments of a fuel cell system, and it presents additional insights into the fundamental aspects of the fuel cell conversions. Theories are presented and tested in practical situations with the objective of generating innovative ideas for future high temperature fuel cell systems.