Bone loss and bone fractures are common complications after organ transplantation. Many factors contribute to the pathogenesis of transplant osteoporosis, such as bone disease preceding transplantation, immunosuppressive medications, and nutritional and lifestyle factors. This study aimed to assess the incidence of vertebral fractures before and after lung and heart transplantation. This longitudinal study analyzed 213 electronic medical records of patients who underwent lung transplantation (n = 128) and heart transplantation (n = 85) at Siena University Medical Center between January 2000 and December 2018. In lung and heart transplant recipients, the bone mineral density in the femoral sub-regions show a significant decrease at post-transplantation and at follow up visits. In both lung and heart recipients, we found an increase in the fracture incidence in the first period after transplantation (19.5% vs. 50.4% in lung recipients; 9.6% vs. 25.7% in heart recipients). Moreover, in lung recipients, vertebral fractures were predicted primarily by age, BMD at the femur, and any history of fracture. In heart recipients, vertebral fractures were predicted only by history of fracture. Our study supports the recommendations for pre-transplant osteoporosis screening in patients undergoing lung transplants, and in the first period after transplantation in heart transplant recipients.