The case is presented of a 71 year-old male, diagnosed with a thymoma. A thoracoscopic thymectomy was performed using the carbon dioxide insufflation technique in the mediastinum. During the procedure, while performing one-lung ventilation, the patient's respiration worsened. The contralateral lung had collapsed, as carbon dioxide was travelling from the mediastinum to the thorax through the opened pleura. Two-lung ventilation was decided upon, which clearly improved oxygenation in the arterial gases and airway pressures. Both pH and pCO2 stabilized. The surgical approach and the carbon dioxide technique were continued because 2-lung ventilation did not affect the surgical procedure. This technique has many serious complications and it should always be performed using 2-lung ventilation.