Spinal cord injury (SCI)-induced bone loss represents the most severe osteoporosis with no effective treatment.Past animal studies have focused primarily on long bones at the acute stage using adolescent rodents.To mimic chronic SCI in human patients, we performed a comprehensive analysis of long-term structural and mechanical changes in axial and appendicular bones in adult rats after SCI.In this experiment, 4-month-old Fischer 344 male rats received a clinically relevant T13 contusion injury.Sixteen weeks later, sublesional femurs, tibiae, and L4 vertebrae, supralesional humeri, and blood were collected from these rats and additional non-surgery rats for micro-computed tomography (μCT), micro-finite element, histology, and serum biochemical analyses.At trabecular sites, extreme losses of bone structure and mechanical competence were detected in the metaphysis of sublesional long bones after SCI, while the subchondral part of the same bones showed much milder damage.Marked reductions in bone mass and strength were also observed in sublesional L4 vertebrae but not in supralesional humeri.At cortical sites, SCI induced structural and strength damage in both sub-and supralesional long bones.These changes were accompanied by diminished osteoblast number and activity and increased osteoclast number and activity.Taken together, our study revealed site-specific effects of SCI on bone and demonstrated sustained inhibition of bone formation and elevation of bone resorption at the chronic stage of SCI.