We demonstrate F-19 and C-13 NMR assignments and study of the structure in solution of Nafion, a perfluorosulfonate ionomer. Using F-19-C-13 HSQC, F-19-C-13 CIGAR-HMBC, and F-19-F-19 COSY to the model compounds of Nafion, we determine 19F and 13 C assignments of model compounds. The combination of the three 2D NMR experiments represents an entirely new approach to analysis of perfluorinated organic compounds. On the basis of the assignments of the model compounds and also based on F-19 coupled and F-19 complete decoupled C-13 NMR for Nafion, F-19 and C-13 NMR assignments are determined for Nafion. In this study the two C-13 signals (OCF2) in the side chain separate more clearly relative to previously reported results. We also carried out MALDI-MS for Nafion, supporting the results found in NMR. From the result of NMR, it is suggested that the aggregates of Nafion in solution exist, and the structure of the aggregates is estimated.