The objective of this study was to compare how cyclophosphamide (CY) and oral busulfan (BU) therapies, each in combination with total body irradiation (TBI), affect the outcome of stem cell transplantation in patients with advanced myelodysplastic syndrome. This study was conducted with 31 patients who received bone marrow from an HLA-matched sibling and underwent treatment with BU-TBI (n = 18) or CY-TBI (n = 13). The incidence of acute graft-versus-host disease (GVHD) grades II to IV was higher, but not significantly, in the BU-TBI group (58.8%) than in the CY-TBI group (30.8%). However, the incidences of chronic extensive GVHD were significantly different (41.7% [CY-TBI] versus 80.0% [BU-TBI], P = .04). Trends after BU-TBI conditioning indicated a lower 3-year probability of disease-free survival (DFS) (38.1% versus 53.9%, P = .4), lower relapse rates (28.5% versus 36.4%, P = .8), and higher nonrelapse mortality rates (46.7% versus 15.4%, P = .2). After adjusting for the International Prognostic Scoring System risk group and the cytogenetic risk group, DFS in the CY-TBI group (relative risk, 9.0; 95% confidence interval, 1.5-52.5; P = .015) was found to be significantly increased compared with the BU-TBI group. Approaches to minimize transplantation-related toxicity should be pursued, and efforts other than the potentiation of the conditioning regimen should be made to reduce the likelihood of posttransplantation relapse.