The aim of this study was to articulate the potential of medical computed tomographic (CT) scanning for analyzing soil structure (macroporosity, soil matrix density, number of macropores) and how these estimates compare with, and complement, traditional laboratory measurements (bulk density, total porosity, effective air-filled porosity, and air permeability). Undisturbed soil cores were sampled at two depths (0.35 and 0.7 m) in a long-term soil compaction experiment in southern Sweden 14 years after its establishment. Persistence of subsoil compaction was detectable by CT-estimated soil matrix density, bulk density, and total porosity. Vertical distribution of CT-estimated air-filled macroporosity between 0.25- and 0.45-m depth showed that biological activity effect on macroporosity was largest in the top of the soil columns from the compacted plots, whereas reduction of macroporosity was significant at the bottom of the same columns. This was not detectable by classical laboratory measurements. Variations in air permeability could be related to the CT-estimated number of pores but not to the CT-estimated air-filled macroporosity. Despite using a coarse resolution, the combination of visualization and traditional laboratory measurements proved valuable in identifying the persistent effects of subsoil compaction and the differences in soil structure among the two investigated subsoil layers. However, we recommend to systematically perform a sensitivity analysis to the segmentation threshold before any further analysis of CT-estimated parameters.