Allogeneic hematopoietic stem cell transplantation (HSCT) remains the only curative therapy for patients with juvenile myelomonocytic leukemia (JMML). The optimal pre-transplantation therapy with maximum efficacy and minimal toxic complications remains a matter of debate. This retrospective study demonstrates single center experience of pre-transplant therapy by hypomethylating agent in children with JMML. Overall, 33 patients were included in analysis. Improved outcome was observed in patients that received pre-transplant AML-like therapy+hypomethylating agents (HMA), AML-like therapy, low-dose chemotherapy ±HMA, only HMA (OS=83%, 44%, 43%, 0%). We have demonstrated that loss of heterozygosity (LoH) of HLA is an important determinant of sensitivity to adoptive immunotherapy and indication for second allo-HSCT.