Bone loss and fractures are common and serious complications following hematopoietic stem cell transplantation (HSCT), and identifying risk predictors for fractures in transplant recipients remains challenging. The Taiwan Bone Marrow Donation Center is the largest databank of donors in Asia. However, no population-based studies have yet been conducted in Asia to accurately assess the risk of fractures. The aims of this study were to determine the incidence and risk factors for fractures in HSCT recipients. We conducted a retrospective cohort study of patients >18 years who received a HSCT from January 1, 2003 to September 30, 2015 using the Taiwan National Health Insurance Research Database. Fractures following HSCT were identified using ICD-9-CM codes. Cox regression analysis was used to identify risk factors for fractures. A total of 3327 patients underwent a HSCT, of whom 126 (3.8%) had a fracture after HSCT. The cumulative incidence of fractures was 5.3% at 5 years, and 10.8% at 10 years. Multivariate analysis showed that a fracture in the 3 years prior to transplant (HR = 3.79; 95% CI 2.39-6.03) was associated with a higher risk of fractures post HSCT. With a daily dose equivalent of >0.50-3.75 mg, >3.75-15.23 mg and >15.23 mg prednisolone, the risk of fractures increased by 1.70 (95% CI 1.07-2.71), 2.23 (95% CI 1.32-3.76) and 2.93 (95% CI 1.43-6.01) folds, respectively. Regular screening to monitor bone loss should be initiated early, and counseling about the importance of general preventive measures for bone loss is warranted in HSCT recipients with a prior fracture and mean daily dose of steroids >0.50 mg.