One of the keys to optimizing polymer-electrolyte-fuel-cell performance is understanding it’s transport phenomena. This is especially critical in the polymer electrolyte in both the bulk and in particular the catalyst layers, where it exists as thin, nanometer-thick film covering the catalyst agglomerates. In these structures, it is known to perhaps inhibit performance, especially as the total platinum content is reduced. Interactions of the membrane with the local environment and as a thin film within the CL result in highly complex material behavior that is highly dependent on the environmental conditions, ionomer thickness, and the material interactions, e.g., carbon, platinum, etc. Thus, characterization of the role of ionomer in fuel-cell catalyst layers requires understanding the transport properties and water-uptake behavior throughout a wide thickness range. In this talk, the role of the ionomer and its underlying structure/function relationships will be elucidated. Ex-situ testing of the catalyst-layer ionomer demonstrates reduced water content for both Nafion and the short-side-chain, lower equivalent weight 3M ionomer. These studies are complemented by thin-film structural and swelling measurements using x-ray scattering and ellipsometry, respectively, which likewise show reduced water content and phase separation as the film thickness decreases. This decrease is caused by an increase in the packing of the polymer chains resulting in increases in mechanical modulus. In addition, direct measurement of the permeability of thin-films is accomplished, again showing that the thin films may result in substantial mass transport limitations. Acknowledgement The authors thank Steve Hamrock and Mike Yandrasits from 3M for helpful discussion and ionomer samples as well as Kunal Karan, Kirt Page, Chris Stafford, and Mike Hickner for discussions. This work made use of facilities at the Advanced Light Source (ALS), supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy. This work was funded by the Assistant Secretary for Energy Efficiency and Renewable Energy, Fuel Cell Technologies Office, of the U. S. Department of Energy under contract number DE-AC02—05CH11231 and a CRADA with Toyota Motor Company.