To remove liquid water from a gas diffusion layer (GDL) effectively and minimize an increase of transport resistance, hydrophobic treatment with a polytetrafluoroethylene (PTFE) is widely used. Because the GDL micro-structure has strong impact on transport properties, detailed understanding of fiber and porous network and PTFE distribution is strongly requested. To investigate correlation between the GDL micro-structure, PTFE treatment, and transport properties, micro-structure of the GDL was visualized by high-resolution X-ray computed tomography (X-ray CT). Newly designed sample holder allowed to regulate compression pressure. Visualization results with spatial resolution of 1.0 μm made it possible to distinguish carbon fibers, binder material, PTFE, and voids (air), and non-uniform distribution of PTFE was observed. Because non-uniform porosity and contact angle distribution in the direction of thickness change the liquid water morphology within the GDL, understanding and controlling the GDL micro-structure is important and manufacturing process of GDL should be scientifically developed.