The study of the behaviour of fuel cells by using various in-situ and ex-situ diagnostic methods is a main topic at the German Aerospace Center (DLR). The degradation of cell components of polymer electrolyte fuel cells (PEFC, DMFC) and of solid oxide fuel cells (SOFC) are of special interest. For this purpose physical and electrochemical methods are used individually as well as in combination. In addition to routinely applied electrochemical methods different methods for locally resolved current density measurements by means of segmented cell technology and integrated temperature sensors have been developed. The latest development with segmented bipolar plates based on printed circuit boards (PCB) is used both in single PEFC cells and stacks. Furthermore, a measuring system for segmented SOFC cells has been developed allowing for the spatially resolved characterisation of cells in terms of current density/voltage characteristics, impedance spectroscopy data, operating temperature and gas composition. The paper summarises the capabilities at DLR with respect to the analysis of fuel cells’ behaviour and gives examples of analytical studies to discuss the potentials and limitations of the diagnostic methodology that is applied.