One-hundred and forty patients who had received HSCT for MDS or AML transformation following treatment of severe aplastic anemia (SAA) were identified in the EBMT database. The median age at HSCT was 29 years (1-66). Donors were related in 49% and unrelated in 51% cases. The 5 years probability of relapse and non-relapse mortality was 17% and 41%, respectively. The five-year overall survival was 45 + 9%, better for patients untreated or in remission than in patients with refractory disease. Allogeneic HSCT leads to prolonged survival in close to half of the patients transforming to MDS or AML from SAA.