Allogeneic stem cell transplantation (alloSCT) is the treatment of choice in the majority of young patients with advanced stages MDS if they have a suitable donor. Since outcome of transplantation is superior for patients with a low blast percentage, this supports the use of chemotherapy prior to transplantation in patients with high blast marrow infiltration. The allogeneic transplant procedure continues to carry a high treatment-related risk, but results have improved progressively over the years. The transplantation results using phenotypically matched voluntary unrelated donors have improved impressingly, mainly due to significantly reduced transplantation-related mortality rate. The upper age limit for transplantation has moved to 65-70 years after the introduction of reduced intensity conditioning regimens (RIC). The place of RIC remains to be determined also in older patients in view of the associated higher relapse risk. For patients lacking a suitable donor the choice is ambiguous. Although the number of reports on autologous stem cell transplantation is still limited, the outcome seems similar to allogeneicSCT with donors other than HLA-identical siblings. Further development of accurate prognostic classification systems will allow a risk-adapted strategy for an individual patient.