Purpose of review Myelodysplastic syndromes (MDSs) are rare disorders in children, showing peculiar clinical manifestations and biological features. This review will summarize biological, genetic and clinical features of childhood MDS and will provide an update of the algorithm of treatment of the different disease variants. Recent findings The most recent classification of MDS includes refractory cytopenia of childhood (RCC), advanced and therapy-related MDS. Importantly, in children, these clonal hematopoietic disorders may be often associated with inherited bone marrow failure syndromes, this representing a challenge for diagnostic work-up and treatment. Moreover, germline syndromes predisposing to develop MDS/acute myeloid leukemia have been recently identified, such as those caused by mutations in GATA2, ETV6, SRP72 and SAMD9/SAMD9-L. Summary Treatment of childhood MDS varies according to specific disease features; allogeneic hematopoietic stem cell transplantation (HSCT) using a Human Leukocyte antigen (HLA)-identical donor, whenever available, represents the treatment of choice for most of these children. HSCT is indicated in MDS with excess of blasts, or in therapy-related MDS. For RCC patients, HSCT is recommended for RCC associated with monosomy 7, or complex karyotype and for patients showing severe neutropenia or transfusion dependence. Novel approaches of HSCT from an HLA-haploidentical relative after selective graft manipulation allow reducing transplant-related complications.