We report molecular-level quantification of chemical degradation of perfluorosulfonated acid (PFSA) ionomer membranes. This is made possible by determining the structure of Nafion 211 using calibrated F-19 magic angle spinning nuclear magnetic resonance spectroscopy upon exposure to hydroxyl radicals. Individual segments of the ionomer were monitored to show that the backbone is resistant to hydroxyl radical attack and that degradation occurs solely on the side chain, with most significant attack occurring toward the end of the side chain. The method provides a means to evaluate changes in chemical structure of PFSA ionomers with a much higher degree of certainty than previously possible.