A 44-year-old male patient was diagnosed with acute lymphoblastic leukemia (CD10+, CD19+, CD20 weak) and underwent unrelated bone marrow transplantation (uBMT) with a conditioning regimen of cyclophosphamide plus total body irradiation during first complete remission (CR). Twenty months post-uBMT, the serum creatinine level (Cre) increased gradually, up to ≥ 1.5 mg/dl at 23 months. Since the increase in Cre was observed continuously, imaging examinations were performed and showed significant bilateral enlargement of the kidneys. Renal biopsy showed diffuse invasion of TdT, CD10 and CD19 positive lymphoid cells in the tubulo-interstitial region. Since leukemia cells were observed in the bone marrow, it was diagnosed as relapse in the bone marrow and kidney. Following reinduction chemotherapy, both kidneys returned to normal size. The patient entered into a second CR, but relapse occurred 6 months thereafter. The patient underwent uBMT again with a reduced-intensity conditioning regimen and CR has been maintained up to 5 months post-second uBMT. Although it is considered rare for relapse to occur with diffuse enlargement of both kidneys, as shown in this case, it is important to confirm the state of the kidney by performing blood tests and image diagnosis during the early phase, when renal dysfunction of an uncertain cause occurs after transplantation.