Near-surface disposal of radioactive waste in shales is a promising option to safeguard the population and environment. However, natural faults intersecting these geological formations can potentially affect the long-term isolation of the repositories. This paper characterizes the physical properties and mineralogy of the internal fault core structure intersecting the Opalinus Clay formation, a host rock under investigation for nuclear waste storage at the Mont Terri Laboratory (Switzerland). We have performed porosity, density, microstructural and mineralogical measurements in different sections of the fault, including intact clays, scaly clays and fault gouge. Mercury intrusion porosimetry analysis reveal a gouge that has a pore network dominated by nanopores of less than 10 nm, yet a high-porosity (21%) and low grain density (2.62 g/cm3) when compared to the intact rock (14.2%, and 2.69 g/cm3). Thus, a more permeable internal fault core structure with respect to the surrounding rock is deduced. Further, we describe the OPA fault gouge as a discrete fault structure having the potential to act as a preferential, yet narrow, and localized channel for fluid-flow if compared to the surrounding rock. Since the fault gouge is limited to a millimetres-thick structure, we expect the barrier property of the geological formation is almost not affected.