Soil structure and particularly the formation of (micro)aggregates are important for long term sequestration of Soil Organic Carbon (SOC). However, research during the last 50 years produced only a few quantitative studies that consider the interactive effects between soil biota and soil physical processes which are especially relevant on the micro-scale. These interactions in turn are primarily dependent on the spatial arrangement of solids and voids since the geometry and continuity of the pore-network within soil aggregates determine the flux of air, water and nutrients and hence control the environment for micro organisms. Advances in synchrotron X-ray tomography and the development of algorithms to quantitatively describe porous media from reconstructed 3D images will greatly facilitate soil structure analysis on the micro-scale. This in turn contributes to understanding the mechanism involved in carbon sequestration within soil intra-aggregate pore space. To provide a statistical analysis of pore geometrical properties pore throat size, channel length and connectivity as well as pore size distributions within aggregates may be useful. Lindquist and Venkatarangan (2000) have developed a suite of algorithms assembled into a software package referred to as 3DMA to extract such geometric property distributions from 3D data sets. The authors investigated the accuracy of their algorithms using a simulated image of packed hexagonal spheres. Relative errors between theoretical and numerically computed values were in general smaller than 5%. Also the analysis of microtomographic images of Fontainebleau sandstone produced good results (Lindquist and Venkatarangan 2000). To test the applicability of above mentioned algorithms for soil aggregates we have analysed a set of soil aggregates approximately 5 mm across at the synchrotron radiation source in Hamburg/Germany (DESY). From the reconstructed 3D images we extracted brick shaped subvolumes which we analysed for pore statistical properties. Potential applications and drawbacks of the applied algorithms will be discussed.