The technique of high resolution electron microscopy has been used to examine the structure of several multilayer systems (MLS) on an atomic scale. Mo/Si multilayers, in use in a number of x-ray optical element applications, and Mo/Si multilayers, of interest because of their magnetic properties, have been imaged in cross-section. Layer thicknesses, flatness and smoothness have been analysed: the layer width can vary by up to 0.6nm from the average value, and the layer flatness depends on the quality of the substrate surface for amorphous MLS, and on the details of the crystalline growth for the crystalline materials. The degree of crystallinity and the crystal orientation within the layers have also been investigated. In both cases, the high-Z layers are predominantly crystalline and the Si layers appear amorphous. Amorphous interfacial regions are visible between the Mo and Si layers, and crystalline cobalt suicide interfacial regions between the Co and Si layers. Using the structural measurements obtained from the HREM results, theoretical x-ray reflectivity behaviour has been calculated. It fits the experimental data very well.