A 72-year-old woman had been diagnosed as having organizing pneumonia at another hospital. She was treated with antibiotics, bronchodilators and prednisolone, but her cough, fever and inflammatory signs were not resolved completely. She was admitted to our hospital for further evaluation of the lung lesion. The chest CT scan revealed narrowing of the segmental bronchus and the serum samples showed elevated MPO-ANCA but negative PR3-ANCA levels. Physical examination also revealed marked bilateral episcleritis and eyeground angitis. Fiberoptic bronchoscopy showed bilateral marked stenotic segmental bronchi associated with mucosal erosions and small nodular lesions. Bronchial and renal biopsy specimens demonstrated marked angitis in the bronchial arteries and glomeruli. A generalized form of Wegener's granulomatosis (WG) was diagnosed and was treated with 60 mg/day of prednisolone, 50 mg/day of cyclophosphamide and 4 g/day of sulfamethoxazole-trimethoprim, which resulted in a marked improvement of the clinical symptoms and endobronchial lesions. In WG, the incidence of endobronchial involvement is 16 to 55% and that of positive serum MPO-ANCA alone is only 14.3%. The present case of WG was considered a rare case with WG which because of the MPO-ANCA-positive but PR3-ANCA-negative findings associated with marked endobronchial lesions and systemic angitis.