Vertebral fractures may result in pain, loss of height, spinal instability, kyphotic deformity and ultimately increased morbidity. Fracture risk can be estimated by vertebral bone mineral density (BMD). However, vertebral fractures may be better defined by more selective methods that account for micro-architecture. Our aim was to quantify regional variations in bone architecture parameters (BAPs) and to assess the degree with which regional variations in BAPs affect vertebral fracture strength. The influence of disc health and endplate thickness on fracture strength was also determined. The soft tissue and posterior elements of 20 human functional spine units (FSU) were removed (T9 to L5, mean 74.45+/-4.25 years). After micro-CT scanning of the entire FSU, the strength of the specimens was determined using a materials testing system. Specimens were loaded in compression to failure. BAPs were assessed for 10 regions of the vertebral cancellous bone. Disc health (glycosaminoglycan content of the nucleus pulposus) was determined using the degree of binding with Alcian Blue. Vertebrae were not morphologically homogeneous. Posterior regions of the vertebrae had greater bone volume, more connections, reduced trabecular separation and more plate-like isotropic structures than their corresponding anterior regions. Significant heterogeneity also exists between posterior superior and inferior regions (BV/TV: posterior superior 12.6+/-2.8%, inferior 14.6+/-3%; anterior superior 10.5+/-2.2%, inferior 10.7+/-2.4%). Of the two endplates that abutted a common disc, the cranial inferior endplate was thicker (0.44+/-0.15 mm) than the caudal superior endplate (0.37+/-0.13 mm). Our study found good correlations between BV/TV, connective density and yield strength. Fracture risk prediction, using BV/TV multiplied by the cross sectional area of the endplate, can be improved through regional analysis of the underlying cancellous bone of the endplate of interest (R(2) 0.78) rather than analysis of the entire vertebra (R(2) 0.65) or BMD (R(2) 0.47). Degenerated discs lack a defined nucleus. A negative linear relationship between disc health and vertebral strength (R(2) 0.70) was observed, likely due to a shift in loading from the weaker anterior vertebral region to the stronger posterior region and cortical shell. Our results show the importance of considering regional variations in cancellous BAPs and disc health when assessing fracture risk.