Since children with myelodysplastic syndromes (MDS) and myeloproliferative disorders (MPD) have a poor prognosis and conventional chemotherapy did not prove to be effective in eradicating them, paediatric patients affected by these diseases and with an HLA-histocompatible donor are to be considered elective candidates for allogeneic transplantation of haematopoietic stem cells (HSC). For those patients with a compatible sibling relapse remains the most important problem, whereas in children transplanted from alternative donors graft rejection and transplant-related mortality significantly contribute to treatment failure. A detailed analysis on the different patient, disease and treatment factors correlated with transplant outcome in childhood MDS and MPD is discussed.