A 47-year-old woman complaining of shortness of breath was referred to our hospital from a nearby clinic. Computed tomography (CT) revealed multiple bilateral pulmonary cysts and bilateral pneumothorax, which were more marked on the right. Chest drains were inserted bilaterally, but the pneumothoraxes did not improve. Thus, the pulmonary cyst in the right lung was resected using video-assisted thoracic surgery. Based on the evidence of bilateral multiple pulmonary cysts, lymphangioleiomyomatosis (LAM) was suggested as a differential diagnosis.However, immunostaining of the resected pulmonary cysts did not reveal LAM. The patient had a history of dermal surgery for hamartomatous lesions, including a fibrofolliculoma on the lower jaw removed 4 years previously. Birt-Hogg-Dubé (BHD) syndrome was suspected, despite no personal or family history of the disease. Genetic testing revealed the presence of a pathogenic variant in exon 11 of FLCN, leading to a diagnosis of BHD syndrome. Our findings highlight the importance of genetic testing based on clinical features even in cases with no family history of the disease, as long as the patient provides informed consent.