Knowledge on the geometry of pore networks of intra-aggregate soil pore spaces are of great value for many soil environmental processes. Advances in non-invasive 3D imaging techniques such as synchrotron-radiation-based microtomography offer an excellent opportunity to study the interrelationship of the pore network geometry with physical processes at a spatial resolution of a few micrometers. This paper presents results of a quantitative 3D pore space geometry analysis of small scale (~5mm across) soil aggregates from contrasting soil management systems. Soil aggregates have been scanned at the SR-μCT facility operated by the GKSS Research Center at HASYLAB / DESY (Hamburger Synchrotron Strahlungslabor / Deutsches Elektronen Synchrotron) in Hamburg/Germany. The achieved isotropic voxel resolution of the scans ranged from 2.4 to 5.4 μm. Three-dimensional reconstructions of the soil aggregates were analysed for various pore space features using a suite of algorithms based on mathematical morphology. Results have shown expected differences in distributions of pore size, throat size, channel length and width as well as tortuosity and connectivity of the intra-aggregate pores with potential implications for soil functions. Underlying image transformations and methods of visualization and quantification of soil pore networks will be discussed in view of their robustness and possible application of such information in soil related research fields.