Substantial progress has been made in the understanding of the pathophysiology of the myelodysplastic syndromes. More refined prognostic classification systems have allowed more individualized treatment programs, leading to improved survival, but not at the expense of the quality of life of the patient. Recent data indicate that some high-risk myelodysplastic syndrome (MDS) patient categories, even some that only achieve partial remissions, may benefit from intensive cytotoxic treatment and may experience long-term survival. Newer chemotherapeutic regimens, eg, containing the mdr less sensitive Idarubicine, the purine analog fludarabine, or such hypomethylating agents as Decitabine, can lead to higher morphologic, cytogenetic, and molecular remission rates, providing a window of opportunity for the assessment of different forms of subsequent stem cell transplantation. Allogeneic stem cell transplantation from sibling donors remains the treatment of choice for younger intermediate and high risk patients with MDS. Much controversy, however, surrounds the applicability of this technique—certainly when using unrelated donors—as first line approach in younger low-risk patients with MDS. This has much to do with the often unacceptably high transplant related mortality rates. Autologous stem cell transplantation may provide a suitable alternative for those patients without a suitable sibling donor or for older patient categories. Peripheral blood progenitor cell collections and transplantations are feasible and carry a low transplant related morbidity and mortality. Prospective randomized studies are underway to assess the true value of intensified chemotherapy with stem cell support in MDS. Childhood MDS is a rare disease, and the data on intensified cytotoxic treatment and transplantation are scarse. However, preliminary data are encouraging.