In the Upper Cretaceous-Danian North Sea chalk, silica composed of nano-size quartz spheres is dispersed in the chalk matrix, and quartz is present in bands and nodules of flint. In the present investigation of the North Sea Danian chalk the nano-quartz in the chalk matrix is compared with the silica in the flint. Samples of chalk and flint layers from four North Sea wells have been investigated. Atomic Force Microscopy (AFM) has been applied to image the quartz in the chalk and in the flint. X-ray diffraction (XRD), including analysis of the positions and profiles of hkl reflections in powder diffraction patterns, has been applied to characterize the lattice of the quartz in both the chalk matrix and in the flint. The quartz in the chalk matrix and in the flint is composed of nano-quartz spheres having identical cell parameters. Based on the results we propose a new model for formation of flint in North Sea chalk: (1) The nano-quartz in the flint, like the nano-quartz in the chalk matrix, has crystallized in the marine Chalk Sea environment. The colloidal quartz particles flocculated and were deposited on the sea floor mixed with calcitic bioclastic material. (2) Regional variations in the concentration of nano-quartz particles in the sediment reflect different degrees of acidification of the Chalk Sea. (3) This resulted in areas where practically all the calcite bioclasts were dissolved leaving a high concentration of nano-quartz particles to form flint layers; where there was less dissolution, indurated chalk with abundant nano-quartz particles is now preserved. (4) The acidification could have been caused by the effects of enhanced atmospheric CO2 linked to massive short-lived volcanic eruptions in the British Tertiary Igneous Province.