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Objective To explore the clinico-pathological features, immunophenotype, treatment and prognosis of urologic primary primitive neuroectodermal tumor (PNET). Methods The clinical data of 3 patients with urologic PNET were analyzed retrospectively. All patients were male, aged 29, 32 and 75 years respectively. Two of the lesions were located in the kidney, and the third was located in the bladder. The sizes of renal tumors were 7.7 cm×6.2 cm and 12.6 cm×9.4 cm respectively. Imaging examinations revealed a well-defined mass with inhomogeneous echo inside. The size of bladder tumor was 10.0 cm×10.0 cm. CT scan demonstrated irregular thickening of the bladder wall, and the density of the wall was inhomogeneous. In the 2 cases of renal PNET radical surgery was performed, while an emergency palliative surgery to remove a blood clot and biopsy were performed in the bladder PNET case. Results In light microscope, the tumors were characterized by uniform small round or oval cells and nest-like or dense sheet structures surrounded by sparse fibrovascular stroma. Homer-Wright rosettes or pseudorosettes were observed, as well as mitoses. Immunohistochemical study revealed that all cases showed positive staining for CD99, synaptophysin and vimentin. One of the renal tumor cells showed positive for CD56, and the other renal tumor and urocystic tumor cells were focally positive for chromogranin A. Additionally, in 1 of the cases of renal tumor there was a high positive rate of 80% for Ki67 staining while the other case showed less than 5%. All 3 cases were eventually diagnosed as PNET. The first renal tumor case was not treated with radiotherapy and chemotherapy postoperatively, and the patient died of recurrence 14 months after surgery. Both the second renal tumor case and the bladder tumor case underwent chemotherapy postoperatively, and they died 4 and 6 months after surgery respectively. Conclusions The urologic primary PNET is a very rare, highly malignant soft tissue tumor, and the diagnosis must be based on pathologic findings and immunohistochemical phenotypes. The multimodal treatment for urologic primary PNET consists of surgery, chemotherapy and radiotherapy.