We studied 91 patients with granulomatosis with polyangiitis (GPA; Wegener’s granulomatosis) who were dealt with by otolaryngologists in Japan. The upper respiratory tract (URT) alone was involved in 56%. Regarding findings of PR3-ANCA, histology and initial diagnosis, of the 40 patients in whom sites other than the URT were involved, 64 and 73 % were positive for PR3-ANCA and histology, respectively. On the other hand, of 51 patients in whom only the URT was involved, only 49 and 31 % were positive for PR3-ANCA and histology, respectively. With regard to diagnosis, definitive and probable diagnoses were made in 78 and 20 %, respectively, of patients involving sites other than the URT. On the other hand, definitive and probable diagnoses were made in only 22 and 37 %, respectively, of patients involving the URT alone; the Japanese diagnostic criteria were inapplicable to 41 %. Of the 21 patients to whom the diagnostic criteria were inapplicable, 13 (62 %) developed additional symptoms and signs during the observation period, and they then fulfilled the Japanese diagnostic criteria. Among these patients, 8 were MPO-ANCA-positive and 3 patients had 2 or more sub-lesions in the URT. If the diagnostic criteria included cases with MPO-ANCA (±) and 2 lesions in the URT, the diagnostic rates increased from 59 to 86 % even though they were of limited form. Thus, about 60 % of the patients with URT symptoms alone did not satisfy the Japanese diagnostic criteria at the initial visit.