Background and aims: With rising survival of neonates, the need for surgical intervention and mechanical ventilation are also increasing. Neonates with mechanical ventilation may have problems related to the intubation. In this study, we aimed to evaluate the factors leading to complications among the intubated neonates after surgery. Materials and Methods: Twenty three newborns with surgical pathologies, who required endotracheal intubation and mechanical ventilation after surgery, were enrolled in the study between January 2008 and December 2008. The gestational age, diagnosis, duration of intubation, associated congenital abnormalities, intubation difficulties and respiratory problems after the extubation were recorded. Results: The mean gestation age was 34 weeks. Congenital diaphragmatic hernia was present in four neonates. There were 5 patients with esophageal atresia and tracheoesophageal fistula, 3 patients with intestinal perforation due to necrotizing enterocolitis and 2 patients with omphalocele. Three patients (with diagnosis of bladder exstrophy, neonatal cholestasis, cystic adenomatoid malformation) having pneumothorax were also included into the study. The mean length of intubation was 8.8 days. Intubation difficulty was encountered in two patients. One patient had extubation failure due to laryngeal stenosis, laryngomalacia and laryngeal granulation. In four patients (17.3%) subglottic stenosis, laryngeal granulation, stridor and laryngomalacia developed. Endoscopic dilatation and excision of granulation tissue were performed in two of them. The other two patients were managed conservatively. All four patients were extubated successfully. Two patients -without extubation problems- died due to multiple organ failure. Conclusion: Endotracheal intubation, extubation and mechanical ventilation are safe procedures in neonates with surgical pathologies if they are performed by the stuff with experience. Follow up of these patients must be achieved in NICU. Complications may occur due to intubation and mechanical ventilation and these problems may require a surgical repair.