Although allogeneic transplantation has resulted in long-term disease-free survival in some patients with myelodysplastic syndromes (MDS), the morbidity and mortality of this approach remains high. Additionally, many patients are not candidates for such an approach because of their age or comorbid factors. Autologous transplantation and the use of reduced intensity conditioning prior to allogeneic stem cell transplantation has provided less toxic alternatives as well as increased the numbers of patients eligible for some form of transplantation. While bone marrow transplantation clearly has a role in the treatment of MDS, the decision to proceed to transplantation is not always easy and the optimal approach has not been clearly defined. Improvement in patient selection and novel approaches to transplantation will hopefully allow for more effective, less toxic results.