Pediatric hematopoietic stem cell transplantation (SCT) has been well established. Recent advances in the transplantation conditioning regimens and in the stem cell sources allow us to increase the candidates for transplantation, but the actual number of pediatric SCTs has been decreased because of the decline in the pediatric population and the progress of various chemotherapies and molecular targeted therapies. Pediatric SCT has become rather sophisticated. Cord blood (CB) stem cell transplantation has the problem of rejection and high relapse rate in the advanced malignant diseases. To overcome the rejection and relapse, it is important to select CB with a large number of the cells and the HLA-mismatched CB. Reduced intensity preparative regimens are increasingly adopted to reduce the early and late transplantation-related complications. In the pediatric setting, reduced intensity transplantation is still under investigation. Late complications for pediatric SCT, growth failure and secondary malignancies should be considered for the increasing number of long-term survivors.