Minimally invasive surgery has been one of the most important surgical advances in the last 15 years. The development of smaller instruments has allowed pediatric surgeons to apply this rapidly evolving technology to neonates. Congenital neonatal deformities including tracheoesophageal fistula, patent ductus arteriosus, duodenal atresia and anorectal malformations are now being managed with minimally invasive surgery. This article summarizes the status of these techniques in neonates.