Fanconi anemia is an inherited bone marrow failure syndrome characterized by chromosomal instability. Hematopoietic stem cell transplantation (HSCT) is considered to be the unique curative therapy of Fanconi anemia. We retrospectively studied 41 pediatric patients with Fanconi anemia who underwent HSCT from December 1996 to March 2009 in 9 centers of Republic of Korea. Twenty patients (49%) received HSCT from unrelated donors, 7 (17%) from related donors and 2 (5%) from haploidentical parent donors. Umbilical cord blood transplantation was performed in 12 patients (29%). Cyclophosphamide and anti-thymocyte globulin were used in 40 patients (98%). Fludarabine and body irradiation were administered to 28 patients (68%) and 21 patients (51%), respectively. Neutrophil engraftment occurred on a median of 12 days after transplantation. Grade II to IV acute graft-versus-host disease (GVHD) developed in 16 patients (39%). Chronic GVHD developed in 7 patients (19%). Thirty patients (73%) were alive with a median of 35 months after transplantation. The transplant-related mortality rate was 27%. The overall event-survival rates differed by donor type : 79% with HLA-matched unrelated donors, 67% with HLA-identical sibling donors, 50% in HLA-haploidentical parent donors and 25% with umbilical cord blood. The event-free survival rates differed by histocompatibility between donors and recipients: 72% with HLA-matched donors, 38% with HLA-mismatched donors ( P=0.029). The cumulative incidence of transplant-related mortality by one year after HSCT was higher in standard dose of fludarabine (100-180mg/m2) group (19%) compared to that in high dose of fludarabine (over 180mg/m2) group (60%) ( P=0.019). HSCT with HLA-matched donors provides high disease-free survival rates and the best means for a curative therapy of Fanconi anemia. The intensity of conditioning should be properly titrated to minimize treatment-related toxicity.