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Opalinus Clay is considered a potential host rock for radioactive waste disposal. The Jurassic claystone formation is composed of several facies and subfacies types, which are characterized by varying amounts of quartz, carbonates (cements and fossils) and clay minerals. To provide samples for ongoing experimental and numerical studies, a complete core section was drilled in the Mont Terri rock laboratory. The lithological and structural variability (including tectonic fault structures) from borehole BAD-2 was investigated using a multidisciplinary approach including high-resolution geoelectric in situ borehole measurements, mineralogical/geochemical and (micro)structural analyses.The lithological–compositional variability was captured by successfully applying a modified subfacies approach, which is independently confirmed by the geochemical data and ERT (Electrical Resistivity Tomography) measurements. The variability on the cm to dm scale perpendicular to bedding can be determined based on the mean resistivity and variation of amplitude. In particular, the facies transitions could be precisely located. The new results suggest that both shaly facies types form the homogenous part of the investigated section, whereas the sandy facies and especially the carbonate-rich sandy facies represent the more heterogeneous lithofacies types of the Opalinus Clay. The varying resistivity can be attributed to differences in clay mineral and carbonate content. Regarding the structural variability, brittle faults were observed with varying frequency throughout the investigated section. Most fault planes occur in the shaly facies types, some of them concentrate along heterogeneities on the subfacies scale. The striking reproducibility of the measurements and observations was confirmed by a comparison with boreholes drilled in parallel, indicating a rather low compositional–structural variability parallel to bedding. The applied multidisciplinary approach is well suited to depict the vertical and lateral variability of a claystone formation, allowing an assessment of the degree of homogeneity/heterogeneity based on the subfacies concept.