In proton exchange membrane fuel cells (PEMFCs), gas diffusion layers (GDL) are crucial for fuel cell performance and more specifically for the removal of the product water where the microporous layer (MPL), as one component of the GDL, plays a significant rule. X-ray computed tomography was applied for the 3D imaging of a gas diffusion layer - Sigracet GDL 35 BC - at sub-mu m resolution to improve the knowledge of its 3D microstructure. The study was focused on the identification of the MPL material within the GDL A segmentation based on a simple gray level thresholding is not appropriate as the gray level ranges for air, carbon fibres and MPL overlap. Consequently, more sophisticated approaches for segmentation were tested; diffusion filtering followed by a gray level thresholding gave the best results. Using this approach, fractures in the MPL layer could be visualised and it was also shown that the MPL can penetrate far into the GDL (C) 2013 Elsevier B.V. All rights reserved.