A 39-year-old woman was referred to our hospital because of pneumothorax related to menstruation. Chest X-ray showed right pneumothorax. Right thoracoscopy revealed 3 fenestrations on the diaphragm. Partial resection of the diaphragm including these lesions were performed. Intrathoracic minocycline was applied expecting pleural adhesion after surgery. Histopathological examination confirmed the presence of endometriosis on the resected diaphragm.