Detailed investigation of the relationship between the physical structure and electrochemical activity of state-of-the-art fuel cell electrodes is a critical, yet often poorly reported or proprietary, step in the manufacturing of cheaper and more durable configurations. Here we demonstrate the utility of X-ray micro-computed tomography (MicroCT) for detailed characterization of the architecture and buried interfaces of fuel cell electrodes in a non-destructive fashion. We employ a combined thresholding and filament tracing based analytical protocol for image analysis which enables more accurate quantification of GDE structures as compared to previously-used thresholding-only methods. Furthermore, we report on a methodology of combining in-situ electrochemical analysis in a microfluidic fuel cell and ex-situ structural analysis in a MicroCT which enables direct correlation of changes in electrode performance to changes in physical structure, in this case, porosity. As a demonstration, the effects of electrode compression are investigated. We observed that both subtle shifts in structure in the microporous and catalyst layers at low compression pressures (<1 x 10(3) lb(f)) and more drastic structural densification of the macroporous carbon fiber layer at moderate compression pressures (>= 1 x 10(3) lb(f)) impact electrode performance. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.033203jes] All rights reserved.