A recently completed deep drilling campaign, comprising 9 deep boreholes penetrating the Mesozoic sedimentary sequence of northern Switzerland, yielded >6 km of drillcore. One of the main objectives was to characterise the low-permeability sequence with the lower Jurassic Opalinus Clay in its centre, motivated by the site selection for a deep geological repository for radioactive waste. In this context, the chemical and isotopic composition of the porewater, as well as the mineralogical and petrophysical properties of the rocks, were among the main study targets. In this paper, the main objective was the characterisation of the lithologically diverse Jurassic rock sequence with focus on mineralogy, porosity and pore-space architecture. Given the large amount of data, a well constrained relationship between clay content (relating to fine-grained sheet-silicate minerals) and porosity could be established. Porosity increases with clay content along a concave curve, but in detail minor formation-specific differences of the positions relative to the best-fit curve were identified. These are attributed to the highly variable deposition rates that resulted in different times available for early diagenesis to alter the rock fabric by mineral dissolution and cementation, thereby affecting the compaction behaviour. Pore-size distributions were obtained from N2 ad-/desorption isotherms. A distinct peak at a radius of 3 nm can be clearly correlated with clay minerals, whereas limestones are dominated by pore sizes in the range of 40–100 nm, and marls show intermediate distributions. A conceptual framework is proposed distinguishing a nanometric porosity that is proportional to the clay content and a contribution of larger pores that are related to the geometric incompatibility between platy clay minerals and isometric calcite or quartz. The contribution of these larger pore is thought to explain the curvature of the clay content-porosity relationship and the more limited compaction of the clay in pressure shadows adjacent to the larger grains. A number of outliers towards high porosity at a given clay content were identified in oolites (most strongly in Fe-rich oolites), sandstones and a unit containing coral-reef material. All these units have in common the presence of competent calcite or quartz grains at the time of deposition, leading to grain-supported fabrics and therefore to a more limited compaction in the interstitial pore space.