In this paper we present a new 3D segmentation approach for the vertebrae of the lower thoracic and the lumbar spine in spiral computed tomography datasets. We implemented a multi-step procedure. Its main components are deformable models, volume growing, and morphological operations. The performance analysis that included an evaluation of accuracy using the European Spine Phantom, and of intra-operator precision using clinical CT datasets from 10 patients highlight the potential for clinical use. The intra-operator precision of the segmentation procedure was better than 1% for Bone Mineral Density (BMD) and better than 1.8% for volume. The long-term goal of this work is to enable better fracture prediction and improved patient monitoring in the field of osteoporosis. A true 3D segmentation also enables an accurate measurement of geometrical parameters that can augment the classical measurement of BMD.