In this study, we present microstructural characterization for polymer electrolyte fuel cell (PEFC) cathodes with low platinum group metal (PGM) loadings together with polarization data analysis. Three-dimensional pore morphology and ionomer distribution are resolved using nano-scale X-ray computed tomography (nano-CT). Electrode structural properties are reported along with the effective ion and reactant transport properties. The characterization results are incorporated with two-dimensional multi-physics model that accounts for energy, charge, and mass transport along with the effect of liquid water flooding. Defining total mass transport resistance for the whole polarization curve, contributions of transport mechanisms are identified. Analysis of the experimental polarization curves at different operating pressures and temperatures indicates that the mass transport resistance in the cathode is dominated by the transport processes in the electrode. It is shown that flooding in the electrode is a major contributor to transport losses especially at elevated operating pressures while the pressure-independent resistance at the catalyst surface due to transport through the ionomer film plays a significant role, especially at low temperatures and low catalyst loading. In addition, by performing a parametric study for varying catalyst loadings, the importance of electrode roughness (i.e, electrochemically-active surface area/geometric electrode area) in determining the mass transport losses is highlighted. (c) 2017 The Electrochemical Society. All rights reserved.