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Background: Dehiscence of esophageal anastomosis is frequent and there are still controversies which type of anastomosis is preferred to diminish its incidence . Aim: To compare end-to-end anastomosis versus end-to-side anastomosis in terms of anastomotic leakage, esophageal stricture and gastroesophageal reflux symptom. Methods: This study was carried out for two year starting from 2012. End-to-side and end-to-side anastomosis were compared in terms of anastomotic leakage, esophageal stricture, gastroesophageal reflux symptom, length of surgery and pack cell infusion. Results: Respectively to end-to-end and end-to-side anastomosis, duration of surgery was 127.63±13.393 minutes and 130.29±10.727 minutes (p=0.353); esophageal stricture was noted in two (5.9%) and eight (21.1%) cases (p=0.09); gastroesophageal reflux disease was detected in six (15.8%) and three (8.8%) cases (p=0.485); anastomotic leakage was found in five (13.2%) and one (2.9%) cases (p=0.203); duration of neonatal intensive care unit admission was significantly shorter in end-to-end (11.05±2.438 day) compared to end-to-side anastomosis (13.88±2.306 day) (p<0.0001). Conclusion: There were no significant differences between end-to-end and end-to-side anastomosis except for length of neonatal intensive care unit admission which was significantly shorter in end-to-end anastomosis group.