Background: Encephalopathy is the most common neurologic complications after organ transplantation and associated with significant morbidity. The aim of this study is to analyze the incidence and characteristics of encephalopathy in overall transplantations including hematopoietic stem cell and solid organs. Methods: We retrospectively analyzed 663 pediatric patients (339 with hematopoietic stem cell transplantation [HSCT], 202 liver transplantation [LT], 55 heart transplantation [HT] and 67 kidney transplantation [KT]) at Asan Medical Center between January 2000 and July 2014. Results: Of the 663 patients, fifty-two patients (7.8%) experienced encephalopathy following transplantation. The incidence of encephalopathy was significantly different after each transplantation; 13 of 55 (23.6%) after HT, 18 of 202 (8.9%) after LT, 5 of 67 (7.5%) after KT, 16 of 339 (4.7%) after HSCT) (p 0.001). Hypertensive encephalopathy (n = 20/52, 38.5%) was the most common etiology in all types of transplantation, followed by drug (immunosuppressant or chemotherapy) induced encephalopathy (n = 15/52, 28.8%), metabolic encephalopathy (n = 11/52, 21.2%), cerebrovascular complication (n = 9/52, 17.3%) and CNS infection (n = 4/52, 7.7%). Drug induced encephalopathy was the most common etiology after HSCT, while hypertensive encephalopathy was the most common after KT and HT and metabolic encephalopathy was most common after LT. The time of onset was also different from each transplantation, median, 5 days after KT (range, 0-491 days), 10 days after HT (1-296 days), 50 days after HSCT (9-1405 days), and 55 days after LT (1-2029 days) (p = 0.021). Mortality rate among patients with encephalopathy was 21/52 (40.4%). Only four patients were died of encephalopathy, all of them had intracerebral hemorrhage. Conclusion: Encephalopathies after transplantation have different characteristics in their incidence, the time of onset, and etiologies according to the types of transplantation. For early detection and proper management for encephalopathy after transplantation, differentiated posttransplantation neurological monitoring for each organ is required.