Compacted MX-80 bentonite is a potential backfill material in radioactive waste depositories. The pore space of these materials is controversially debated. 3D reconstructions of the pore space based on tomographic methods could provide new insights into the nature of the pore space of compacted bentonites. To date, such reconstructions are largely absent due to problems related to the preparation of bentonite samples for electron microscopy. As a contribution to ongoing discussions, the nanoscale intergranular pore space was investigated by cryo Focused Ion Beam nanotomography (FIB-nt) applied to previously high-pressure frozen MX80 bentonite samples. This approach allowed a tomographic investigation of the in-situ microstructure related to different dry densities (1.24, 1.46 and 1.67 g/cm3). FIB-nt is capable to resolve intergranular pores with radii > 10 nm. With increasing dry density (i.e. 1.24 to 1.67 g/cm3) the intergranular porosity (> 10 nm) decreased from about 5 vol.% to 0.1 vol. %. At dry densities of 1.24 and 1.46 g/cm3 intergranular pores were filled with clay aggregates, which formed a mesh-like structure, similar to the honeycomb structure observed in diagenetic smectite. In contrary to “typical” clay-gels, the cores of the honeycomb structure were not filled with pure water, but instead were filled with a less dense material, which presumably consists of very fine clay similar to a colloid. In the low-density sample this honeycomb-structured material partly filled the intergranular pore space but some open pores were also present. In the 1.46 g/cm3 sample, the material almost completely filled the intergranular pores. At the highest investigated densities (i.e. 1.67 g/cm3) the honeycomb-structured material was not present, which is likely due to the lack of intergranular pores. The latter was interpreted to suppress the formation of a honeycomb framework or skeleton composed of clay aggregates.