Electron microscopy of nervous tissue requires on the one hand nanometre resolution for the analysis of fine structures of nerve cell contacts, for instance synaptic vesicles, synaptic membranes and associated organelles. On the other hand, the visualization of the three-dimensional organization of nervous tissue on the level of dendrites and neurites is essential for the understanding of neuronal integration and also for a stereological evaluation of quantitative parameters such as size and shape of synaptic contact zones, number and distribution of synaptic vesicles, organization of cytoskeleton and distribution of organelles like mitochondria and endoplasmic reticulum. Therefore, it is necessary to have access to the fine structure and to the spatial organization within one sample. Energy-filtering transmission electron microscopy (EFTEM) enables the imaging of sections up to 1 micron thickness with a high resolution because the chromatic error due to inelastic scattering is avoided by selecting electrons within a restricted energy-loss range for imaging. The contrast depends strongly upon the section thickness, the selected energy range and the composition of the sample, so that optimum imaging conditions can be found for each object. Different staining protocols enable either a high global contrast or a selective staining of peculiar tissue properties. The three-dimensional organization can be visualized with stereopairs or with extended tilt series, which shows that characteristic structures as the synaptic junctions are detectable only within a narrow range of orientations to the electron beam. This is especially important for quantitative approaches with stereological tools which profit generally from the fact that a wide range of section thickness is available with EFTEM. EFTEM is therefore a powerful tool for the imaging of thick sections of biological materials with attractive possibilities of contrast tuning and advantages for stereological quantifications. The main benefit is the rapid and effective visualization of the three-dimensional organization of cells and tissues.