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A 69-year-old man who had undergone an esophagectomy was diagnosed with chylous leakage on postoperative day 2, and his pleural effusion output gradually increased daily. On postoperative day 6, intranodal lymphangiography using lipiodol demonstrated chylous leakage from branches of an incomplete duplicated left-sided thoracic duct; it also indicated successful ligation of the right-sided thoracic duct at initial operation. After lymphangiography, the chylous leakage did not heal and remained uncontrollable. Based on the preoperative lymphangiographic findings, we ligated the left-sided thoracic duct with left-sided video-assisted thoracoscopic surgery, with the patient in the prone position, on postoperative day 9. The patient experienced no other postoperative complications. The use of the prone position with pneumothorax treatment was helpful in providing a wide operative field in the posterior mediastinum, thus allowing for a better chance for a successful postoperative outcome.