The exploration of soil structure and its consequences for ecological functions is of prime importance for understanding of the “critical zone.” In soils, the relationship between soil structure and plant roots—which influences water dynamics in soil—deserves special interest. With X-ray computed microtomography (micro-CT), soil structure and roots may be visualized and quantified simultaneously. We analyzed undisturbed soil samples from three grassland sites. After scanning the soil cores with an X-ray micro-CT scanner (resolution 40 μm), roots were delineated from the soil material and soil pore space by means of their X-ray grey value characteristics followed by the use of space transformation during image analyses. To determine efficacy of the X-ray micro-CT to identify roots, root volumes and surfaces were quantified with a standard root washing method showing good correspondence. A strong positive correlation between root volume and surfaces and the solid surface/solid volume ratio was found, with greater root growth in a more aggregated and porous soil. Preliminary analyses suggest that the relationship between soil structure and root patterns is related to the intensity of land management at the grassland sites, with reduced root volumes and surfaces at sites with increased land use intensity. This methodology has substantial potential for further research on management influences on soil structure and root growth across landscapes.