Based on system tests, a model-aided system analysis tool is developed to model different types of fuel cell systems. In the experimental modeling approach, a model system which is general and flexible is parameterized on the basis of data measured from a system. The aim of this model is to obtain information concerning the efficiency of the system and its individual system components, to reveal problems during operation and to analyze the potential for optimization. A first evaluation of the procedure is performed on a 2 kW(el) and 4 kW(thenal) Polymer Electrolyte Membrane fuel cell (PEMFC) Combined Heat and Power (CHP) prototype system, installed at the Institut fur Werkstoffe der Elektrotechnik (IWE), Universitat Karlsruhe (TH). The system, which was developed at the Zentrum. fur Sonnenenergie- und Wasserstoff-Forschung ZSW, Ulm (FC stack) and the Fraunhofer-Institut fur Solare Energiesysteme ISE, Freiburg (natural gas reformer) is operated and tested in close cooperation with the Stadtwerke Karlsruhe. The CHP system including the measurement equipment, as well as the modeling and simulation approach based on system tests are presented.