The aim of this study was to evaluate the swallowing problems by fiberoptic endoscopic evaluation of swallowing (FEES) study in both short- and long-gap patients after esophageal atresia (EA) repair. Hospital records of patients who had undergone surgery for EA were reviewed retrospectively. Patients were divided into two groups as short-gap (SG) group (n:16) and long-gap (LG) group (n:10) to compare the swallowing problems. FEES study was performed, and the results were discussed in detail. There were twenty-six (16M/10 F) patients with a mean age at evaluation was 7.52 ∓ 3.68years. Mean follow-up period was 75.35 ∓ 44.48months. In FEES study, pharyngeal phase abnormalities were detected in 10 patients (38.4%). Pharyngeal phase abnormalities were detected significantly higher in LG group (p:0.015). Laryngeal penetration/aspiration was seen in four patients on FEES study (15.3%). All of them was in LG group (40%). Laryngeal penetration/aspiration was seen significantly higher in LG group (p:0.014). This is the first study to conduct FEES study in children after esophageal atresia repair to evaluate their swallowing conditions. Even though our sample is small, swallowing problems are more common than expected in the cases of LG when compared to SG.