Mudstones are one of the least permeable rocks in most sedimentary sequences. Accordingly they can act as seals for fluid flow leading to abnormal overpressures. Nevertheless, mudstone compaction and related permeability and porosity decrease are not adequately described in current basin modelling software, because only mechanical compaction is taken into account. In reality, however, clay minerals undergo severe chemical diagenesis which certainly influences petrophysical properties and compaction. In this context a mathematical approach which has been originally developed in soil mechanics has been adapted to basin modelling. The underlying mathematical equations are carefully explained in the text. In the basic equation the compression coefficient is a function of void ratio and effective stress. Using these equations, overpressure can be predicted by using petroleum systems modelling techniques. This is shown for a real 3D case study in the North Sea, in which strong overpressure occurs. A compaction model for mudstones that depends strongly on the clay content of the individual stratigraphic units is used for the calibration of porosities in the 3D case study. In addition, a chemical compaction model that reduces porosities by using a kinetic reaction is used for the deeper part of the basin where mechanical compaction processes are less important. The pressure generation process depends strongly on permeability and compressibility of the porous medium. Therefore, the use of mudstone compaction and permeability models is sufficient to produce pore overpressures. In the case studied, abnormal overpressures are generated during burial together with the petroleum generation process. The mechanical and chemical compaction mechanisms ensure that the pressures are preserved in the deeper part of the basin.