Trabecular bone architecture is one of the main factors influencing the mechanical behavior of cancellous bone. To assess the three-dimensional trabecular microstructure of intact bones, we introduced the concept of noninvasive bone biopsy, a method to assess and analyze cancellous bone based upon three-dimensional peripheral quantitative computed tomography in vivo (3D-pQCT). The aim of this work was to demonstrate the potential of noninvasive bone biopsies as a basis for structural and mechanical analysis of trabecular bone in the process of rapid bone loss. A group of six healthy young male volunteers was measured to provide data on the reproducibility of structural parameters. Baseline and 1-month follow-up measurements were performed to provide data on short-term precision of the procedure, and three of the controls were reanalyzed within 3-6 months to estimate long-term precision. Prior to structural evaluation, the baseline and follow-up measurements were repositioned three-dimensionally to ensure matching volumes of interest (VOI). Trabecular bone density (TBD) as well as structural indices were analyzed for all measurements. The VOIs were analyzed morphometrically by evaluating bone volume (BV/TV) and trabecular number (Tb.N) based on a direct three-dimensional approach. Trabecular thickness (Tb.Th) and trabecular separation (Tb.Sp) were derived from these two indices. The data of the measurements at 1 month to determine the short-term precision was in excellent agreement with the baseline measurements. The results showed that structural parameters can be reproduced in vivo with a coefficient of variation of less than 0.5%. With a typical spread of 4% for the structural indices within the group of healthy volunteers, an intraclass correlation of better than 0.98 was reached. We conclude that high-resolution 3D-pQCT has the potential to detect structural changes in trabecular bone during therapeutic and diagnostic trials.