In this work, micro-computed tomography (mu CT) imaging is presented as a novel and robust tool for characterizing the surface roughness andmorphological properties of polymer electrolytemembrane (PEM) fuel cell gas diffusion layers (GDLs). Commercially available paper and felt GDLs with varying degrees of hydrophobic treatments and microporous layer (MPL) coatings were characterized. GDL surface height data was obtained from high resolution three-dimensional (3D) mu CT reconstructions (2.44 mu m-wide voxels), where large samples (approximately 4.5 mm x 4.5 mm) were used in order to capture the roughness features of the GDL, MPL crack depths, MPL crack widths, and MPL crack lengths. A sensitivity study reveals the significance of sample size and surface height thresholding on roughness parameters in this work. Therefore, the authors warn that caution must be exercised when selecting surface roughness measurements for modelling applications and that scanning size and resolution should correspond to the phenomena that are being investigated. (C) 2016 The Electrochemical Society. All rights reserved.