OBJECTIVE A single center study was conducted to compare the short-term clinical outcome between laparoscopic surgery (LS) and open surgery (OS) repair for neonates with congenital duodenal obstruction (CDO). METHODS Medical records of all neonates with bodyweight at surgery over 1500g and without other gastrointestinal anomalies that underwent surgery (duodeno-duodenostomy or duodeno-jejunostomy) for CDO at our center between January 2009 and July 2015 were reviewed. The choice of OS or LS was surgeon-dependent. RESULTS One hundred twelve patients were identified, with a median age and weight at surgery 8.5days and 2500g respectively. Forty-four patients underwent OS and 68 patients LS. There were no significant differences between the two groups regarding patient age, gender, weight at surgery, associated anomalies, and mean operative time. Compared to OS, the LS group had lower postoperative complications (5.9% vs 36.4%, p<0.0001), shorter mean time to initial oral feeding and mean postoperative hospital stay (3.9 vs. 7.1days and 8.6 vs. 12.9days respectively, p<0.0001) and better postoperative cosmesis. CONCLUSIONS LS treatment for neonatal CDO is associated with lower postoperative morbidity, shorter recovery time and postoperative hospital stay and better postoperative cosmesis than OS. METHODS Retrospective Comparative Study. METHODS Level III.