Stem cell transplantation (SCT) from a histocompatible sibling is treatment of choice for severe aplastic anemia. Survival rates have been reported to be as high as 90% for children. Immunosuppressive therapy (IST) is employed in patients who are not candidates for SCT due to donor unavailability. The addition of cyclosporin A to antilymphocyte globulin has improved the response rate to 70-80%, and survival at 5 years among responders is about 90%. In all, 30% of patients treated by IST suffer from relapse, but long-term prognosis does not appear to be affected by this complication. Juvenile myelomonocytic leukemia (JMML) shares both myelodysplastic and myeloproliferative features. Survival (10-year) of patients with JMML without SCT is only 6%. Children with JMML should be transplanted early in the course of their disease. Conditioning regimen composed of three alkylating agents, busulfan, cyclophosphamide and melphalan has been favored by the EWOG-MDS and EBMT-Pediatric WP in the second half of the 1990s. SCT using this conditioning regimen is capable of curing approximately 50% of patients with JMML. More than 70% of patients with refractory cytopenia and more than 50% of children with advanced MDS are cured of by the early performed allogeneic SCT.