Wegener's granulomatosis is a rare disease that pathologically causes necrotizing granulomatous vasculitis in the arterioles and venules and it can invade the whole body. In addition, it is difficult to distinguish between a nontuberculous mycobacteria infection that shows manifestations of granuloma and Wegener's granulomatosis. There has been no reported on a patient who had the 2 abovementioned two diseases at the same time. A 69 year old male patient had Wegener's granulomatosis that had invaded the prostate. He also had a scrotal swelling and back pain. He had manifestations of granulomatous infection on the scrotum and spine biopsies. However, there was no clinical evidence of Wegener's granulomatosis. As a result, we examined him for other diseases that can cause a granuloma. Consequently, he was also diagnosed as suffering with a nontuberculous mycobacteria infection. We report here on this case and we review the relevant medical literature.