In the oil fields in the Central Graben of the North Sea, Maastrichtian chalk is an important hydrocarbon reservoir, but oil may also be found in the Danian chalk, consisting of white chalk interbedded with clay layers. Within the chalk section, discrete intervals appear like chalk but contain large amounts of quartz (up to 100%). The aim of the present investigation is to reveal the mechanism for formation of the quartz in these intervals and to discuss their regional distribution and importance for the reservoir properties. Samples of chalk, including quartz-rich intervals, and clay layers from three wells SA-1, Rigs-1 and Rigs-2 in the South Arne Field have been investigated. Calcite-free residues obtained using a buffered dissolution of calcite were investigated using X-ray diffraction, scanning electron microscopy and atomic force microscopy. The main silica phase in the Upper Cretaceous–Danian chalk in the three wells is a nano-size α-quartz. This has probably formed from Si dissolved from radiolarians in the free-water phase. The 600 Å diameter α-quartz spheres precipitated in the free-water phase with subsequent flocculation of the spheres and sedimentation of the flocs. Variations in the proportion of quartz in the chalk are attributed to variations in the amount of radiolarians in combination with variations in CO2 concentrations in the water; increased CO2 causes dissolution of coccoliths and thus a relative enrichment in quartz. This formation mechanism is regional and makes it probable that the layers rich in nano-quartz may be found over large areas provided that the chalk is authigenic. Quartz-rich layers are generally of low permeability and in areas with authigenic chalk these layers may act as internal seals in chalk reservoirs.