Mucosa-associated lymphoid tissue (MALT) lymphomas are a distinctive group of B-cell lymphomas. These lymphomas arise from various anatomic sites and are mainly seen in the gastrointestinal tract, but the primary involvement of the kidney is extremely rare. We report a case of a MALT lymphoma involving the kidney and the renal pelvis. A 56-year-old man presented with a history of hematuria and left flank pain. A computed tomography scan showed a marked tissue densification in the renal sinus, suggesting marked thickening of the urothelium, conditioning deformity of the renal pelvis and calyces. A cystoscopy confirmed a 2-cm papillary lesion on the left lateral aspect of the bladder. The patient underwent laparoscopic radical nephoureterectomy and transurethral bladder resection. The pathological diagnosis was MALT lymphoma in the kidney and urothelial carcinoma of the bladder. The patient was referred to a hematologist and was free of disease at 20 months of follow up without additional treatment.