Several investigators have been looking for less toxic conditioning regimen for stem cell transplantation in Fanconi anemia (FA) patients because of sensitivity to DNA cross-linking agents and tendency to malignancy. We report 16 multitransfused FA patients who underwent peripheral stem cell transplantation from 13 related and 3 unrelated donors. Although the first 6 patients received thoraco-abdominal irradiation + cyclophosphamide + antithymocyte globulin (regimen A) for conditioning, fludarabine (FLU) + cyclophosphamide + antithymocyte globulin (regimen B) were used in the last 10 patients in which 3 of them received unrelated graft. Cyclosporin A was given alone for the related allografts but also included mycophenolate mofetil for the unrelated allograft as graft versus host disease prophylaxis. We observed a lower risk of peritransplant morbidity and mortality with fewer and milder graft versus host disease in FLU based group. We lost 3 patients in regimen A group and 1 of them from secondary acute myeloid leukemia. Three patients are alive with transfusion independent. In regimen B group, 9 of 10 patients are alive with normal hematologic parameters and full donor chimerism. The longest follow-up durations are 90 and 60 months in regimen A and B, respectively. In conclusion, FLU based conditioning is more effective and successful with lower toxicity in multitransfused FA patients. However, it needs more experience and longer follow up duration.