Investigations of mass movements of the Messel oil shale in Germany presumed that swell- and especially shrink-deformations of the organic-rich clay were among the factors triggering initial displacements. Within the scope of the present studies, delicate clay/organic microstructures had to be deciphered. Reactions of clay minerals and microstructures upon dehydration were observed by environmental scanning electron microscopy (ESEM) and the distribution of organic matter was studied by confocal laser scanning microscopy (CLSM) in fluorescence mode. ESEM and CLSM have been demonstrated to be valuable tools for the microstructural characterization of laminated organic-rich sediments. The application of these analytical and imaging techniques will be of great interest to a wide range of geological disciplines such as palaeontology, organic petrology, engineering geology and global change studies.