A 49-year-old man was diagnosed with autoimmune pulmonary alveolar proteinosis. Chest computed tomography (CT) showed typical CT findings of pulmonary alveolar proteinosis: thickening of septa with ground-glass opacities in both lung fields. The diagnosis of autoimmune pulmonary alveolar proteinosis (PAP) was based on findings of bronchoalveolar lavage (BAL) fluid with milky appearance and elevated serum titer of anti-granulocyte-macrophage colony-stimulating factor antibody. We decided to perform segmental BAL via bronchoscopy. The surgery was performed under a general anesthesia since the patient had severe hypoxemia and strong cough reflex. Following 3 repeated courses of therapy, his respiratory condition and the ground-glass opacity in both lung fields improved remarkably, with no recurrence in 3 years. There are only a few published case reports in the world of the usefulness of segmental BAL under general anesthesia for PAP. We consider that segmental BAL is a useful therapeutic method for PAP in cases with severe hypoxemia, such as the present patient.