An 8-year-old boy was diagnosed with precursor B-cell acute lymphoblastic leukemia. After intensified chemotherapy, he underwent sex-mismatched allogeneic cord blood transplantation. Postcord blood transplantation cytogenetic studies revealed engraftment failure evidenced by switching into the recipient type (XY), and, notably, various complex chromosomal aberrations in the recipient cells. Nonclonal and clonal aberrations including deletions of 7q and 20q were persistently observed. Nonetheless, the patient was clinically stable without evidence of marrow dysplasia or leukemic cells. Del(7q) and del(20q), 2 recurrent chromosomal aberrations in myeloid neoplasia, might represent underlying genomic instability in this patient, not the direct culprits of dysplasia or leukemogenesis.