Hematopoietic stem cell transplantation (HSCT) has been an established as a curative therapy for the various hematologic nonmalignant and malignant diseases in childhood. In addition to conventional indications like hematological malignancies, aplastic anemia and solid tumours, a gerat deal of inborn errors in children can be cured with HSCT. Recent applications and recommendations in terms of stem cell sources, indications, conditioning and post-transplant complications in children like infectious complications, graft versus host disease (GVHD), gastrointestinal and liver complications, pulmonary complications and late endocrine effects are discussed in this review.