The successful development of novel materials for polymer electrolyte membrane fuel cell (PEMFC) electrodes is hindered by the lack of a fundamental understanding of the complex, multicomponent nature of the catalyst layer (CL), the interplay of its components, and their independent and cooperative effects on the effective properties. One of the most prevalent methods for preparing PEMFC membrane-electrode assemblies is the thin film decal transfer (DT) method, which involves dispersing the catalyst powder and perfluorosulfonic acid ionomer in a solvent media to form a catalyst ink, and then forming a porous thin film CL which is then transferred to the membrane via hot-pressing. To achieve maximum performance, the CL needs to have (i) the maximum interface of ionomer and catalyst for the anode and cathode reactions, (ii) the appropriate pore structure to allow gas and water diffusion, and (iii) ionomer networks that bind the carbon aggregates together, providing structural integrity for the catalyst layer and a proton conduction path. For optimization, the type of solvent, solvent-to-solids ratio, and ionomer-to-carbon ratio are variables which affect the resulting CL structure and performance. Characterization of both catalyst inks and catalyst layers is necessary to understand how processing, structure, properties, and performance are all related. In this study, a systematic approach was taken to study the microstructure of the catalyst ink formulations and the prepared CLs using ultra-small-angle X-ray scattering (USAXS). By combining USAXS with small angle X-ray scattering (USAXS-pinSAXS), it is possible to obtain scattered intensity spanning over several decades in scattering vector, q (q = 4πsinθ/l), which can provide size and structural information from 1 nm to 6 mm. USAXS-pinSAXS measurements were performed at the Advanced Photon Source (APS) at Argonne National Laboratory. Multiple-level curve fitting, using a suite of macros written for Igor Pro-based software, was used to extract from the scattering data the particle size, size distribution, and geometry of the carbon-supported Pt and Pt-alloy aggregates in catalyst-ionomer-solvent inks and catalyst layers. The USAXS-pinSAXS study showed formation of aggregated microstructures, which are different for the Pt and Pt-alloy catalyst inks and catalyst layers.