A 58-year-old male was diagnosed as having Philadelphia chromosome-positive acute myeloid leukemia and treated with imatinib combined chemotherapy followed by reduced-intensity cord blood transplantation. After transplantation, the graft was rejected but the Philadelphia-positive leukemia clone was eliminated. Following graft rejection, hematopoietic recovery with del (20q) gradually occurred. These findings suggest that this patient had transformed to acute myeloid leukemia from myelodysplastic syndrome with del (20q) after acquisition of the Philadelphia chromosome.