A 35-year-old male was admitted to our hospital because of a persistent nasal obstruction and headache. In the laboratory findings, inflammatory reactions were seen, and anti-neutrophil cytoplasmic antibody (PR 3-ANCA) was positive. He was diagnosed with Wegener's granulomatosis (WG) based on the above symptoms, PR 3-ANCA positivity and pathology of nasal mucosa. Chest radiogram showed a solitary lung lesion in the apex of the left lung. The patient was treated with steroid and cyclophosphamide. Symptoms and inflammatory reactions were improved dramatically, however, the size of the solitary lung lesion did not change. Video-assisted thoracic surgery (VATS) was performed to differentiate the lesion from neoplasm. It showed features consistent with WG pathologically. The solitary lung lesion in WG is sometimes difficult to differentiate from lung neoplasm in clinical course, if the lesion does not improve by the standard therapy for WG. So in these cases, VATS is needed to confirm these lesions pathologically.