Clay-rich sedimentary rocks are considered as seal lithologies for hosting radioactive waste or as caprocks for geological carbon sequestration sites. Evaluation of the rock's sealing capacity requires a comprehensive understanding of mass transport processes, which, in turn, demands knowledge of the 3D structure of pore space. Here, the use of focused ion beam nanotomography (FIB-nt) in building realistic pore space models is demonstrated along with a novel approach employed to analyze the topology of the pore space. The method was applied to three samples of the Opalinus clay of in northern Switzerland which is considered as a candidate host rock formation for the disposal of radioactive waste. Due to resolution limitations the lower limit of analyzed pore radii was about 10 nm. Pore radii > 10 nm were related to a physical porosity of about 2 vol.%. Comparing the pore size distribution determined by FIB-nt with the one obtained by N₂ adsorption analysis, FIB-nt revealed the structure of about 20% of the total pore space. The total external porosity determined by N₂ adsorption analysis was in the range of 10 to 12 vol.%. Our approach to analyze the complex 3D structure of the pore space was based on converting the voxel based 3D structure into a 3D graph of the pore skeleton. A 3D graph representation permitted determination of the spatial distribution of pore space geometrical properties such as pore path orientation, pore path tortuosity and pore path length. Pore-paths in Opalinus clay show a preferred orientation within the bedding plane in combination with a comparatively low pore path tortuosity. Pore path tortuosity perpendicular to the bedding plane is higher by a factor of as much as five. Anisotropy in pore space is caused by spatial density variations of pore path orientation (i.e. preferred orientations of pore paths) in combination with an elongated pore shape (i.e. low tortuosity).