Osteoporosis affects an estimated 44 million Americans. This condition results from bone loss, but the measured change in bone mass does not fully account for the marked decrease in whole-bone structural integrity seen in osteoporosis. In order to study structural changes in bone mineral distribution due to normal ageing and osteoporosis, we have developed a method for progressive analysis of whole-bone mechanical integrity from helical CT images. The system provides rapid semi-automated alignment of femur and vertebrae volume images into standard anatomic reference planes, and calculates bone mineral density in any selected 3D sections of bone. Mineral density measures are obtained using both full-width-half-max contours and threshold-derived masks, and are obtained for cortical bone and trabecular bone separately. Biomechanical properties of the bone cross-section are also assessed, including the 2-D bending moment of the cortical bone region and the integrated flexural rigidity of the cortical region or whole-bone region in arbitrary planes. This method facilitates progressive refinement of the analysis protocol by separating the labor-intensive alignment and landmark selection process from the analysis process. As the analysis protocol evolves to include new measures, previously analyzed images can be automatically reanalyzed, using the image regions originally specified. Initial results show inverse correlation of indices of biomechanical bone strength with age, greater loss of bone strength in the lumbar spine than in the femoral neck, and more trabecular than cortical bone loss at both sites.