A 9-year-old boy was admitted due to fever for two weeks and lumbago. The laboratory results showed a white blood cell (WBC) count of 3.9 x 109/L with 0% blast cells, and bone marrow (BM) evaluation showed 50% blast cells with lymphoid characteristics. Immunophenotyping confirmed BCP-ALL. Cytogenetic analysis was performed on a BM sample. G-banded chromosome analysis revealed a male karyotype 46, XY, -21, + mar/46, XY. The poor quality of the metaphase chromosomes restricted their evaluation. The FISH study showed no rearrangements in BCR/ABL1, KMT2A, or ETV6/RUNX1. However, FISH revealed 5-12 signals of RUNX1 in 68% of interphase cells (Figure 1A). There was no extramedullary organ infiltration. He was treated according to the Japanese Pediatric Leukemia/Lymphoma Study Group's protocol for the standard-risk group. Peripheral blood showed good treatment response to prednisolone on day 8, and BM examination after the induction therapy revealed complete remission (CR) and negative for MRD detected by a real-time polymerase chain reaction of antigen receptors. Although he had been clinically well for 35 months, he presented pallor and splenomegaly at 11 months after frontline chemotherapy. He had a WBC count of 15.9 x 109/L with 66% blast cells and the morphologic evaluation of the BM showed 97.3% lymphoid blast cells. G-banded chromosome analysis of the BM sample revealed a male karyotype 46, XY, -21, + mar. FISH analysis revealed no ETV/RUNX1 fusion signals and five signals for the RUNX1 probe in 96% of the analyzed nuclei (Figure 1B). There was no extramedullary organ infiltration. He was diagnosed with late isolated BM relapse of iAMP21-positive BCP-ALL and treated according to the ALL-R3 mitoxantrone regimen. He achieved a second CR after induction chemotherapy and MRD in BM after induction was negative. He received two cycles of a 28-day continuous infusion of blinatumomab at 15 mug/m2/day, followed by a 4/6 antigen matched unrelated CBT. The myeloablative conditioning regimen consisted of 12-Gy total body irradiation (TBI) from days -9 to -6 (six fractions), intravenous etoposide 15 mg/kg/day from days -5 to -4, and intravenous cyclophosphamide 60 mg/kg/day from days -3 to -2. Tacrolimus and short-term methotrexate were used for graft-versus-host disease (GVHD) prophylaxis. Neutrophil engrafted on day 23 post-CBT. BM examination post-CBT revealed CR with 100% donor-type hematopoiesis. He experienced grade II acute GVHD involving the skin only, which was successfully treated with an increased tacrolimus dose. He has been in good condition for the last 15 months following CBT without ALL recurrence.