The application of capillary electrophoresis/mass spectrometry was investigated concerning the separation and identification of ionic components generated by degradation of the polymer electrolyte membrane for fuel cells. A model degraded sample was prepared by Fenton oxidation of a Nafion^® membrane. Model and control samples were dissolved in a water/2-propanol (1/1) mixed solution, and used for an investigation. In the mass detection for the anionic components, an unknown compound was observed at m/z 297. The migration behavior of the component in capillary electrophoresis suggested that the component is highly acidic. The structure of the compound was estimated by an analysis of its migration behavior and its mass spectrum. The component was probably generated by a side-chain cleavage of Nafion^®.