Recently, haploidentical hematopoietic stem cell transplantation (Haplo-HSCT) is expected to provide a graft-versus-leukemia (GVL) effect that targets a mismatched HLA haplotype of hematological malignancies with relapse or poor prognosis. It is reported some leukemia patients who relapsed after Haplo-HSCT, lost a mismatched HLA haplotype of leukemic cells. We evaluated a loss of mismatched HLA haplotype by HLA DNA typing using blood samples obtained during relapse for 6 patients who relapsed after Haplo-HSCT. Two of 6 patients showed a loss of mismatched HLA haplotype. It is important to estimate whether the mismatched HLA haplotype derived from leukemic cells exist or not for the decision of therapeutic strategy in recurrent cases after Haplo-HSCT.