Bloodstream infection (BSI) is a recognized cause of morbidity and mortality in children after hematopoietic stem cell transplantation (HSCT). However, there are limited reports on BSI after HSCT in pediatric patients in multiple centers. This study was a retrospective cohort analysis of consecutive patients who underwent allogeneic and autologous HSCT at the Department of Paediatrics, Hokkaido University Hospital, between 1988 and 2009; the Department of Paediatrics, Sapporo Hokuyu Hospital, between 2007 and 2009; and the Department of Paediatrics, Asahikawa Medical University, between 1989 and 2009. A total of 277 patients underwent HSCT during the study period. In this multicenter analysis, cases of BSI after HSCT were recorded in the early posttransplant period (within the first 100 d), and BSI was observed in 24 of 277 HSCT patients. Multivariate analysis showed that nonmalignant disease was an independent factor associated with BSI after HSCT (hazard ratio 6.3 for aplastic anemia or Wiskott-Aldrich syndrome patients; confidence interval, 1.4-12.8; P=0.012). We conclude that aplastic anemia and Wiskott-Aldrich syndrome were the novel risk factors for BSI in pediatric patients after HSCT.