We describe a new method for the direct examination of three‐dimensional bone structure in vitro based on high‐resolution computed tomography (CT). Unlike clinical CT, a three‐dimensional reconstruction array is created directly, rather than a series of two‐dimensional slices. All structural indices commonly determined from two‐dimensional histologic sections can be obtained nondestructively from a large number of slices in each of three orthogonal directions. This permits a comprehensive description of structural variation within a specimen and greatly facilitates the study of structural anisotropy. A measure of three‐dimensional connectivity (Euler number/tissue volume) has been determined for the first time in human cancellous bone and shown to correlate with several two‐dimensional histomorphometric indices. The method has the potential for overcoming many of the limitations of current approaches to the study of bone architecture at the microscopic level.