Allogeneic bone marrow transplantation is an effective treatment for myelodysplastic syndromes, providing a probable cure in about one-third of cases overall. It is generally reserved for patients under 50 years who have an HLA-compatible donor. Post-transplant disease-free survival rates vary according to several prognostic factors, which often overlap with those predicting the spontaneous outcome of the disease. Consequently, it is sometimes difficult to choose the indications and timing of bone marrow transplantation in this setting. Here we review the literature in an attempt to draw up relevant guidelines.