Background: Thoracoscopy has become a surgical option for the repair of esophageal atresia (EA) and congenital diaphragmatic hernia (CDH). Insufflation of carbon dioxide combined with one lung ventilation creates an anesthetic challenge to control acidosis and maintain oxygenation while allowing optimal operative exposure. We have overcome these issues by utilizing the high-frequency oscillating ventilator (HFOV) and report our early experience. Methods: A retrospective review from 2007 to 2010 on neonates who underwent thoracoscopic operation utilizing HFOV. Patient demographics and intraoperative course were reviewed. Results: Seventeen neonates were identified, 12 with EA and 5 with posterolateral CDH. The median age at operation was 4 days (range 1-166 days), with a median weight of 2.9±1.0kg. Median gestational age was 38±3 weeks. Before surgery, 6 patients (35%) were on conventional mechanical ventilation, and no patient was on high-frequency oscillating ventilation. Median American Society of Anesthesiologist's score was 3 (range 3-4). There were no intraoperative complications and median operative time was 208±72 minutes. Review of the operative reports identified no significant difficulties with exposure of the operative field in all patients. Median ventilator manipulations needed were 3 per case. Mean intraoperative pulse oximetry was 97%±2%. Sixteen patients had intraoperative arterial blood gases; 1 had venous sampling. Patients with arterial blood gases had a mean pH of 7.36 (range 7.18-7.47), mean pCO2 was 41mmHg (range 25-63mmHg), and mean pO2 was 156mm Hg (range 41-426mmHg). Conclusion: Usage of HFOV allows for good intraoperative exposure with excellent oxygenation and elimination of carbon dioxide to prevent acidosis. © Copyright 2011, Mary Ann Liebert, Inc. 2011.