Wegener's granulomatosis (WG) is characterized by necrotizing polyangiitis involving the respiratory tract and kidneys. It causes segmental necrotizing glomerulonephritis in the kidneys. In rare cases, a renal pseudotumor may be seen because of the granulomatous process. Association of WG with renal malignancy, however, is very uncommon. We report a case of a patient who presented several years after being treated for WG with malignant hypertension and an infiltrating mass in the right kidney. The histopathology of radical nephrectomy specimen showed presence of primitive neuroectodermal tumor (PNET). Association of renal cell carcinoma (RCC) with WG has been documented in a few cases, but PNET in such circumstances has not been reported. Long-term immunosuppressive treatment is a known risk factor in the development of malignancies, so it is proposed that the occurrence of RCC in WG may have been a side effect of cyclophosphamide treatment. It is not clear whether the same mechanism for PNET holds true in the present case. It is important to make a differential diagnosis between true malignancy and pseudotumors in WG as these entities cannot be distinguished based solely on imaging. We suggest a need to routinely screen the WG patients for increased risk of urologic malignancies.