The myelodysplastic syndrome (MDS) is a rare, clonal disorder of pluripotent stem cells in children and is characterized by ineffective haematopoiesis, morphologic abnormalities in one or more cell lines in a usually cellular bone marrow, and by predilection for the acute leukaemia. A large proportion of children with MDS present associated clinical abnormalities. Allogeneic stem cell transplantation (SCT) is the only definitive cure for this heterogeneous group of lethal disorders. Results with SCT have been difficult to interpret due to the variability of conditioning regimens, types of donors, and pretransplant therapy. In many series, the outcome with donors other than matched siblings has been extremely poor. The optimal pre-transplant therapy and conditioning regimen for SCT in MDS have not yet been defined. The establishment of several international working groups will eventually help to elucidate the pathogenesis of childhood MDS and will evaluate new treatment strategies to improve their clinical outcome.