A 7-year-old girl with acute myelogenous leukemia with multilineage dysplasia received unrelated cord blood transplantation but developed hemophagocytic syndrome (HPS) after sepsis with methicillin-resistant coagulase-negative staphylococci before engraftment. Bone marrow aspiration on day 20 revealed a markedly increased number of activated macrophages showing hemophagocytosis. The presence of donor-type chimera in the bone marrow was confirmed at that time. We therefore quickly started immunosuppressive and antibacterial treatment. Although her condition gradually improved, the patient suffered graft failure due to HPS. She received peripheral blood stem cell transplantation from her HLA 2-loci-mismatched mother on day 54 and continued in complete remission 12 months after the second transplantation. The results in this case suggested that because of fetomaternal microchimerism it may be useful to select an HLA-haploidentical mother as a backup donor for stem cell transplantation.