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We herein report a case of myasthenia gravis (MG) in which thoracoscopic thymectomy was performed for a large thymic cystic lesion using a subxiphoid approach. We have previously suggested the usefulness of the subxiphoid approach in thymectomy. The indications of thoracoscopic thymectomy were recently expanded to include large thymic cystic lesions without intraoperative rupture of the lesions. The pathologic diagnosis of the lesion in the present case was multilocular thymic cyst with type A thymoma and micronodular thymoma. The postoperative complications were minimal without MG crisis. Thoracoscopic thymectomy using a subxiphoid approach seems to be an ideal procedure, even for large thymic cystic lesions. In addition, early-onset MG with a large thymic cystic lesion may suggest the presence of a small thymoma even if the lesion is not detected on a preoperative radiologic examination.