Upper Cretaceous–Danian chalk and interbedded clay-rich layers from wells of the South Arne Field and adjacent wells in the North Sea and from Stevns in Zealand have been investigated to determine the clay mineralogy in the chalk and the origin of the interbedded clay-rich layers. The mineralogy, with emphasis on clay mineralogy, was determined after removal of the calcite by dissolution at pH 4.5–5 in order to preserve the other minerals. Generally, mixed-layer minerals are the dominant clay minerals, except for two wells, Rigs-1 and Rigs-2, where a 3D ordered kaolinite prevails. A detailed structural characterization of the mixed-layer minerals was carried out by modeling of the X-ray diffraction (XRD) patterns. In most of the samples dominated by mixed-layer minerals, two mixed-layer phases, a high-smectite illite-smectite (I-S) and a low-smectite illite-smectite-chlorite (I-S-Ch), prevail, irrespective of depth or location of the samples. However, some samples contain I-S-Ch and ordered S-Ch, and others a chlorite-serpentine (Ch-Sr) phase, and these samples probably formed during diagenesis at higher temperatures. The clay-rich layers and the adjacent chalk have the same or quite similar clay mineralogy, both with respect to kaolinite vs. mixed-layer minerals and with respect to their detailed structure. In conclusion, the kaolinite is detrital and the I-S minerals formed in the chalk from volcanic ash. The main conclusion is that the clay-rich layers in the North Sea chalk formed by dissolution of the calcite in the chalk and that this dissolution took place at burial depths of >1 km, probably through migration of solutions through permeable chalk layers.