In a rare case of bronchogenic cyst with high carbohydrate antigen (CA) 19-9 production, a 57-year-old man with coughing and chest pain was diagnosed with a subcarinal mediastinal tumor. Fiberoptic bronchoscopy showed an erosive mucosal lesion overlying the area of extrinsic compression at the membranous of the right mainstem bronchus. Serum carbohydrate antigen 19-9 was elevated at 1300 U/ml. Thoracotomy showed an encapsulated cyst tightly adhering to the right main bronchus. The cyst was extirpated after ablation at the adherent cystic wall by electrocautery. Although intracystic carbohydrate antigen 19-9 concentration was very high, serum carbohydrate antigen 19-9 and bronchoscopic findings returned to normal postoperatively. The histological diagnosis was consistent with a bronchogenic cyst and carbohydrate antigen 19-9 could be immunohistochemically demonstrated within its epithelium.