A 78-year-old man was referred to Tsukuba University Hospital for right hydronephrosis. He had undergone ureteroscopy and ureteral stenting in another hospital, but no tumor was revealed in renal pelvis and ureter. The urinary cytology was negative. Computed tomography (CT) revealed remarkable thickening of right renal pelvis and ureter wall. CT also showed para-aortic, iliac, supraclavicular and mediastinal lymph node (LN) swelling. 18F-fluoro-2-deoxy-D-glucose positron emission tomography (PET) revealed high uptake at thickened right renal pelvis and ureter wall and enlarged LNs. The soluble interleukin-2 receptor was elevated to 1,110 U/ml (normal range: 613 U/ml). Those findings suggested that the malignant lymphoma originated from the renal pelvis and ureter rather than urothelial cancer. Therefore we performed open biopsy of iliac LN and periureteral tissue. The pathological diagnosis was mucosa associated lymphoid tissue (MALT) lymphoma. The patient was trasferred to the department of hematology, and treated with rituximab and bendamustine. After 6 courses of chemotherapy, swelling of renal pelvis, ureter and LN was markedly reduced. The ureteral sent could be removed. MALT lymphoma of the upper urinary tract is extremely rare and pretreatment diagnosis is difficult. In 8 of 11 reported cases, the diagnosis was made by nephroureterectomy. In our cases, open biopsy could avoid nephroureterectomy.