We suspected Birt-Hogg-Dubé syndrome (BHDS) from intraoperative findings of emergency operation for idiopathic hemopneumothorax. A 34-year-old man was delivered to our center due to sudden chest pain and dyspnea. Under the diagnosis of hemopneumothorax, emergency operation was performed. During surgery, multiple thin wall lung cysts of 2 to 5 mm in size were observed on the surface of all lung lobes. BHDS was suspected, but the surgery was limited to hemostasis and resection of pulmonary cyst since the diagnosis had not been established. Postoperative chest computed tomography (CT) revealed irregular shaped pulmonary cyst on the interlobar, mediastinal and diaphragm surface. Genetic analysis showed deletion in the folliculin gene confirming the diagnosis of BHDS.