Fanconi anemia (FA) is a rare autosomal recessive disease characterized by congenital abnormalities, cancer predisposition and progressive BM failure. FA patients present spontaneous and induced chromosome breakage. Hematopoietic SCT (HSCT) represents the unique therapeutic option to restore normal hematopoiesis when marrow failure or clonal hematopoietic abnormality occurs. Conventional myeloablative conditioning regimen, especially including a high dose of irradiation, appeared strongly toxic for FA patients. Then, reduced-intensity conditioning regimens were developed successfully for those patients. However, TRM still remained higher than for other HSCT indications. The development of fludarabine containing a non-myeloablative conditioning regimen appears to be a major progress. Long-term follow-up is absolutely necessary.