The use of new technologies, especially computer-based three dimensional reconstructions and micro-computer tomography (μ-CT) have greatly improved and facilitated the detailed investigation of insect anatomy. Optimal results in morphological work aiming at phylogenetic reconstruction can be obtained with a combined application of different techniques such as histology, scanning electron microscopy, and μ-CT. The use of μ-CT greatly enhances the efficiency of the acquisition of detailed anatomical data and allows a broad taxon sampling in phylogenetic studies partly or entirely based on morphological characters. A disadvantage of phase contrasted μ-CT images is the poor differentiation of different tissue types. This problem can be overcome by the use of stable low energy photon beams as available at the beamline BW2 of the Deutsches Elektronen-Synchrotron in Hamburg (DESY). Synchrotron-radiation-based μ-CT data (SR μ-CT) obtained with this approach are an ideal basis for highly efficient three dimensional reconstructions of high quality.