Supportive care remains the mainstay of therapy for patients with myelodysplastic syndrome (MDS). Although allogeneic bone marrow transplantation is the only known curative therapy for MDS, its risks make this treatment prohibitive in many patients, who tend to be older and have other medical problems. With advances in hematopoietic stem cell transplantation (HSCT), we can offer transplant to an increasing number of patients. It is, however, necessary to assess each patient and his or her disease individually and evaluate prognostic factors, treatment options, appropriateness of HSCT, and, if appropriate, type and timing of HSCT. We will review the data on HSCT in MDS in order to examine each of these issues and clarify the decision-making process.