Abstract Samples from Rupel Clay across the Netherlands were analysed for the assessment of its heterogeneity in geochemistry and mineralogy. X-ray fluorescence (XRF) and bulk and clay fraction X-ray diffraction (XRD) analyses of 152 samples from 17 different cores are presented and statistically interpreted. The results show a wide variation in the quartz, feldspar, clay mineral and carbonate content between the different samples. Factor analysis showed that the main variance between the samples can be explained by the clay mineral and quartz concentration, the carbonate content and pyrite plus organic matter. In the south of the Netherlands, the Rupel Clay is more quartz-rich and coarse grained. In addition, the clay is heterogeneous, varying with location and depth, consistent with observations for Belgium Boom Clay. Towards the north, the Rupel Clay becomes more clay-rich, finer grained and more homogeneous, both laterally and with depth. In addition, the clay has a relatively high carbonate and organic matter content. The pyrite content does not show any trends with location and depth. The differences between north and south are explained by the variations in depositional setting within the southern North Sea Basin.