STEM-, FIB- and X-ray tomography were applied to a sample taken from the Opalinus Clay unit. This allowed characterization of the pore structure in the fine-grained clay matrix at different levels of microstructural detail. On the level of detail that can be resolved by FIB-nt, the observed pore space is largely unconnected and the resolved porosity was in the 2–3 Vol.% range. At higher optical magnification but for smaller sample sizes, STEM tomography resolved a porosity of around 13 Vol.%. This suggests that the transition from an unconnected to a connected pore space in the shale sample occurs on the few nanometer scale. Geometric analyses of larger pores as visualized by FIB-nt revealed that dilation induced formation of bridges of only a few hundred nanometers between tips of neighboring pores may lead to a coalescence of larger pores. The resulting large pore network may allow for gas transport in the fine-grained clay matrix.