The use of computational methods for the study of clay minerals has become an essential adjunct to experimental techniques for the analysis of these poorly ordered materials. Although information may be obtained through conventional methods of analysis regarding macroscopic properties of clay minerals, information about the spatial arrangement of molecules within the interlayers is hard to obtain without the aid of computer simulation. The interpretation of experimental data from techniques such as solid-state nuclear magnetic resonance or neutron diffraction studies is considerably assisted by the application of computer simulations. Using a series of case studies, we review the techniques, applications and insight gained from the use of molecular simulation applied to the study of clay systems (particularly for materials applications). The amount of information that can be gleaned from such simulations continues to grow, and is leading to ever larger-scale and hence more realistic classical and quantum mechanical studies which promise to reveal new and unexpected phenomena.