Myeloid malignancies in children include de novo acute/chronic myeloid leukemia (AML/CML) and secondary malignancy due to genetic predisposition or previous therapy. Generations of clinical trials for childhood myeloid disorders have resulted in improved disease characterization and outcome, and defined therapeutic strategies combining chemotherapy, biologic response modifiers and immunotherapy. With advancement in molecular genetics and the development of sensitive techniques to detect response, residual disease and relapse, therapy can be tailored in a risk-based manner using clinical and biological/ molecular parameters and several 'good-risk' myeloid malignancies enjoy high cure rates with targeted therapy. However, hematopoietic stem cell transplant remains the best method of treatment intensification for poor-risk disorders such as relapsed/secondary AML, myelodysplastic syndrome and juvenile myelomonocytic leukemia. Indications for transplant and outcomes of previous clinical studies, and novel transplant strategies designed to improve safety and efficacy of the procedure are reviewed.