Pediatric myelodysplastic syndrome (MDS) are a heterogeneous group of clonal disorders often occur in the context of inherited bone marrow failure syndromes, acquired aplastic anemia or gene predisposition. Germ line syndromes predisposing individuals to develop familial MDS or acute myeloid leukemia have recently been identified – mutations in RUNX1, ANKRD, GATA2, ETV6, SRP72, DDX41. Juvenile myelomonocytic leukemia (JMML) occurs in context of inherited and somatic mutations PTPN11, KRAS, NRAS, CBL, NF1. In pathogenesis of these disorders there are a several factors – hypermethylation, clonal hematopoiesis/cytopenia of undetermined significance, disturbances of bone marrow microenvironment, telomeres, immune mechanisms. Allogeneic hematopoietic stem cell transplantation is the main method of MDS and JMML treatment but it is necessary to take into account special indications for refractory cytopenia (infections, dependence on blood transfusions) and be careful for JMML with CBL mutation.