A novel method allows the monitoring of radical formation and membrane degradation in-situ in a working fuel cell which is placed in the microwave resonator of an electron paramagnetic resonance (EPR) spectrometer. By introduction of a spin trap molecule at the cathode the formation of immobilized organic radicals on the membrane surface is observed for F-free membranes, revealing the onset of oxidative degradation. For Nafion® there is much less evidence of degradation, and the hydroxyl radical is detected instead. At the anode, free radical intermediates of the fuel oxidation process are observed. No traces of membrane degradation are detected on this side of the fuel cell.