Ultra-small angle X-ray scattering (USAXS) was employed to investigate the effects of carbon support type, the presence of platinum on carbon, and ionomer loading on the microstructure of polymer electrolyte fuel cell (PEFC) catalyst layers (CLs). Particle size distributions (PSDs), obtained from fitting the measured scattering data were used to interpret the size of carbon aggregates (40–300 nm) and agglomerates (>400 nm) from two-component carbon/ionomer and three-component platinum/carbon/ionomer CLs. Two types of carbon supports were investigated: high surface area carbon (HSC) and Vulcan XC-72. CLs with a range of perfluorosulfonic acid (PFSA) ionomer to carbon (I/C) ratios (0.2–1.2) and also with perfluoroimide acid (PFIA) ionomer were studied to evaluate the effect of ionomer on CL microstructure. The carbon type, the presence of platinum, and ionomer loading were all found to significantly impact carbon agglomeration. The extent of Pt/C agglomeration in the CL was found to increase with increasing ionomer and platinum concentration and to decrease with increasing carbon surface area. Platinum electrochemically-active surface area (ECSA) and local oxygen transport resistance (RnF) were correlated to the CL microstructure to yield relationships affecting electrode performance.