Background. Granulomatosis with polyangiitis (GPA) is a rare disease, and its clinical diagnosis can occasionally be difficult. Case. A 63-year-old woman was examined at our hospital for cough with excessive sputum production. Chest computed tomography (CT) revealed multiple masses in the bilateral lower lobes of the lungs. Bronchoscopy and a CT-guided needle biopsy revealed no significant findings; however, lung cancer was suspected. After 2 months, she developed a fever with a temperature of 38°C on consecutive days. Repeat chest CT revealed enlarged masses with cavitation in the right lower lobe. On repeat bronchoscopy, a histological examination showed multinucleated giant cells, necrotic tissue with neutrophils, and granuloma formation. Elevated levels of serum proteinase-3-antineutrophil cytoplasmic antibody (11.9 U/ml) were found on blood testing. GPA was eventually diagnosed. Conclusion. GPA should be considered in patients presenting with multiple masses in the bilateral lungs.