The intubation of a double lumen endotracheal tube (DLT) has become the technique of choice for most procedures requiring one lung ventilation (OLV). The potential complications of the use of DLT are airway ruptures and malpositions of the DLT which can induce an increase of airway pressure, hypercapnia, severe hypoxemia, and other effects during the induction of general anesthesia. The intractable hypoxia due to total lung atelectasis is one of the very rare complications during and after intubation of the DLT. We experienced a 16 year-old male patient with severe hypoxia scheduled for thoracoscopy after a position change from supine to lateral decubitus. The hypoxia was unable to be easily corrected by endobronchial suction, rechecking of DLT position with fiberoptic bronchoscope, and manual positive ventilation, even after a position change to supine. An emergent chest X-ray revealed total atelectasis of the right lung that was relieved gradually by general supportive care at the intensive care unit.