Peroxide radical treatments of a perfluorinated ionomer used in polymer electrolyte membrane (PEM) fuel cells and its small molecule analogues were carried out, along with analysis of the resultant products. Molecules containing terminal carboxylic acids degraded at least 1 order of magnitude faster than noncarboxylate materials; all of the systems did show peroxide-initiated degradation nonetheless. Product analysis suggests that terminal carboxylic acids react according to a sequential chain shortening, consistent with previous studies. Cleavage of side chains from both polymer and model compounds was also observed to be important and in fact may be the dominate pathway in low carboxyl content commercial PEM membranes, based on the following comparison of reactivity and concentration. The relative reactivities of carboxylic chain ends and ether linkages is approximately 500, as calculated using model compounds fluoride generation rates. Commercial perfluorosulfonic acid (PFSA) products contain minimal carboxylic acid end groups, and the side chain concentrations are of 2-3 orders of magnitude higher than carboxylic acid end groups.