Twenty-three consecutive patients undergoing related-donor BMT for myelodysplastic syndrome (MDS) were conditioned with a combination of busulfan (BU) and cyclophosphamide (CY). GVHD prophylaxis was with cyclosporine (CSP)/methotrexate (MTX) in 15 patients, CSP/methylprednisolone (MP) in six patients, and CSP/MP/MTX in two patients. The most frequent regimen-related toxicities were oral mucosal (87% of patients, 61% > or = grade II) and hepatic (82% of patients, 43% > or = grade II). The overall incidence of grade II-IV acute GVHD was 48% with eight patients dying of acute or chronic GVHD. There have been five relapses, with the cumulative risk of relapse being 35% (95% confidence interval [CI], 16%-66%). Eight patients remain alive and well (median follow-up 27 months, range 15-70 months), with an estimated 3-year event-free survival (EFS) of 35% (95% CI, 17%-54%). Univariate analysis of EFS by pretransplant variables indicated that only age < or = 35 years correlated with a favorable outcome (p = 0.04). BUCY is an effective, well-tolerated alternative conditioning regimen for MDS patients undergoing allogeneic BMT.