Gas diffusion medium (GDM) is a crucial component in proton exchange membrane fuel cells (PEMFCs). Being composed of a gas diffusion layer (GDL) with a micro-porous layer (MPL) coated onto it, it ensures a proper water management due to the highly hydrophobic materials employed in cell assembly. In current commercial applications, the desired water repellent behaviour is usually obtained by using polytetrafluoroethylene (PTFE). In this work, Fluorolink ® P56 (Solvay Specialty Polymers, Milan, Italy), a commercially available, anionic, segmented high molecular weight polyfluorourethane with perfluoropolyether groups was extensively evaluated as an alternative to PTFE for micro-porous layer hydrophobization. A change in polymer used is desirable in order to simplify the production process, both in terms of ink formulation and thermal treatment, as well as to get a higher hydrophobicity and, consequently, more efficient water management. Innovative prepared samples were compared to a PTFE-based GDM, in order to assess differences both from morphological and from an electrochemical point of view.