This article describes a new method to analyze the structural behavior of trabecular bone structure by means of noninvasive measurements of the three-dimensional cancellous bone architecture. For the noninvasive data acquisition, a high-resolution quantitative computed tomography system for peripheral measuring sites (pQCT) was used. With this system and the help of a multiple thin-slice measuring technique, it became possible to examine three-dimensional bone structure with a resolution of 0.25 mm. Using a special three-dimensional segmentation algorithm, mineralized bone was separated from bone marrow and muscle tissue within the three-dimensional stack of CT slices. These segmented data sets can then be processed nondestructively and, even more important, repetitively in either two or three dimensions. In order to validate this noninvasive procedure, a two-dimensional comparative morphometric study was performed including CT slices and corresponding histologic sections prepared after CT measurement. Three representative sections from the three-dimensional stack of CT slices were selected and the morphometric indices of the segmented CT slices were compared with the indices stemming from the corresponding histologic sections prepared after CT measurement. Although the presented approach can only give an example of the method, the results from the morphometric analysis support the assumption that cancellous bone structures based on noninvasive high-resolution CT measurements are representative for trabecular microstructures assessed from histologic bone sections. The study demonstrates the potential of high-resolution CT imaging for in vivo applications of quantitative bone morphometry. This is especially true for repetitive follow-up measurements, which cannot be performed using histologic sections. Additionally, the method offers an easy access to the three-dimensional structure of trabecular bone, which is mandatory for the analyses of the anisotropic mechanical behavior of cancellous bone.