Between March 1973 and August 1990, 17 patients with Fanconi anemia (FA) underwent bone marrow transplantation in Seattle. Marrow donors were HLA identical siblings (n = 14), phenotypically HLA identical parents (n = 2) and a one antigen mismatched parent (n = 1). Patients with no evidence of leukemic transformation (n = 12) were conditioned with 140-200 mg/kg cyclophosphamide (CY). Of five patients with leukemic transformation, four received CY (120 mg/kg) plus 12 Gy fractionated total body irradiation and one patient received busulfan (14 mg/kg) and CY (100 mg/kg). All patients engrafted; however, one patient whose sibling donor's cells showed variable results when assayed for chromosome instability required two additional marrow infusions. Toxicity associated with the conditioning regimen included severe oral mucositis (n = 14), hemorrhagic cystitis (n = 11) and diffuse erythroderma (n = 3). Seven of the 12 patients without leukemic transformation are surviving 1-17 years (median = 5 years) after transplant, with an estimated survival probability at 5 years of 65% (95% CI 0.31; 0.85). Two patients developed squamous cell carcinoma of the tongue greater than 10 years post-transplant. One of these patients died at 10.3 years as a result of the malignant process, and the other is disease free more than 12 years post-transplant. Of the five patients with leukemic transformation, one is alive at 8 years. These data demonstrate that marrow transplantation can offer long-term survival for patients with FA, engraftment can be achieved with reduced doses of CY in FA patients, and less toxic preparative regimens are needed for FA patients who have developed leukemic transformation.