Abstract Fuel cells allow an environmentally friendly and highly efficiently conversion of chemical energy to electricity and heat. Therefore, they have a high potential to become important components of an energy-efficient and sustainable economy. The main challenges in the development of fuel cells are cost reduction and long-term durability. Whereas the cost can be significantly reduced by innovative mass production, the knowledge to enhance the lifetime sufficiently is not available. Surface science analysis methods used for the characterization of the new and used electrodes can be use to determine the alterations in the fuel cell components and in this way to identify the degradation processes, but they do not allow to quantify the influence of the alterations in the electrodes on the electrochemical performance. For this purpose electrochemical methods are necessary; especially the electrochemical impedance spectroscopy (EIS) allows to separate the performance losses individually and to assign them to different components and processes of the cell via a model, whereas the choice of the right model can be problematic. Two important and distinct structural degradation processes were identified by surface analysis of the electrodes before and after fuel cell operation: first, the decomposition of poly tetra-fluoro-ethylene (PTFE) which is used as an organic binder and as a hydrophobic agent in the electrodes and second, a change of the structure of the catalysts. The observed decomposition of the PTFE is associated with a decrease of the hydrophobicity of the electrode. A loss of hydrophobicity influences drastically the required operation conditions and leads to a more critical water management of the fuel cell. In contrast, the alteration of the catalysts structure in the electrodes causes an irreversible decrease of the electrochemical performance. In polymer electrolyte fuel cells (PEFCs) a particle agglomeration of the platinum catalysts at the cathodes is detected. With EIS the effect of two different degradation processes in the membrane-electrode-assembly was quantified. During continuous operation the degradation of the PTFE induces an approximately two times higher performance loss compared with the performance loss related to the agglomeration of the platinum catalyst.