As a part of the European Union BIOMED I study “Assessment of Bone Quality in Osteoporosis,” the trabecular structure of transiliac bone biopsies was assessed by conventional histomorphometry and by three-dimensional microcomputed tomography (μCT). Sixty-three cylindrical human transiliac bone specimens were obtained post mortem from 27 women and 36 men (age 23–92 years) and evaluated morphometrically in this study. For the conventional histomorphometric analysis, a pair of four undecalcified sections were prepared from two regions in the mediolateral plane of the bone cores. The sections were stained with the von Kossa technique to obtain high-contrast two-dimensional images. Prior to the histologic sectioning the samples were measured with a desktop μCT, providing a 14 μm nominal resolution. The morphometric parameters computed by both methods in two or three dimensions, respectively, were bone volume density (BV/TV), bone surface density (BS/TV), trabecular thickness (Tb.Th), and trabecular separation (Tb.Sp). Results showed highly significant (p < 0.0001) correlations between conventional histology and μCT for BV/TV (r = 0.93), BS/TV (r = 0.91), Tb.Th (r = 0.84), and Tb.Sp (r = 0.91). The mean percentage differences between histology and μCT ranged from 2.5% (BV/TV) to 6.1% (Tb.Th). The high correlations and the low differences in terms of absolute numbers between conventional histomorphometric and micro-tomographic analysis are very promising for the use of micro-tomographic imaging. μCT is a nondestructive, fast, and very precise procedure that allows the measurement of cancellous and compact bone in unprocessed biopsies or small bones, as well as a fully automatic determination of three-dimensional morphometric indices.