Hematopoietic stem cell transplantation is increasingly used for treatment of malignant and nonmalignant disorders, genetic and immunologic disorders, and solid tumors. Although advances in immunosuppressive therapy and management of infections have improved long-term survival, transplant recipients remain at risk for a multitude of complications, many of which are serious and life threatening. Posttransplant complications may be classified either according to the organ system or according to the timeframe following transplantation. Complications may involve the chest, abdominopelvic organs, the central nervous system, or musculoskeletal tissues. This article reviews the various clinical and radiologic findings of key complications following hematopoietic stem cell transplantation and the pertinent differentiating factors.