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Background Improved survival of neonates with esophageal atresia with/without tracheoesophageal fistula (EA/TEF) has resulted in increased prevalence of gastro-esophageal and respiratory-related morbidities. However, long-term outcome data on these patients remains limited, making it difficult to substantiate any guidelines on their chronic care. The purpose of our study is to report on their post-operative outcomes especially the long-term gastro-esophageal and respiratory morbidities. Methods This was a retrospective review of 65 patients (39 males, 26 females) who underwent EA/TEF repair from 1996 to 2019 at a single tertiary institution. Follow up data pertaining to clinical characteristics, operative management and long-term gastro-esophageal and respiratory morbidities was analyzed. Results Fifty-seven patients (87.7%) had Gross Type-C anatomy, followed by 5(7.7%) patients with Type-A, 1(1.5%) with Type-B and 1 with Type-D. One patient had a late diagnosis of H-type fistula (Type-E). Thirteen (20%) patients had long-gap EA. Median age at first surgery was day 1 (IQR 1–2) of life. All patients underwent bronchoscopy at their index surgery. All 52 non-long gap EA (LGEA) patients underwent primary anastomosis, while most (76.9%) LGEA patients underwent staged repair. Post-operatively, 4(6.2%) developed anastomotic leak which resolved with conservative management. Three (4.6%) had recurrent TEF, 2 underwent re-do ligation. Twenty (30.8%) patients developed anastomotic strictures, with 15 requiring serial dilatation. Long-term burden of gastro-esophageal and respiratory morbidity was high (63.1%; 64.6% respectively). The majority (n = 39,60%) of patients required active follow-up for a median duration of 5 years (IQR 1.5–10 years). Predominant conditions were gastroesophageal reflux disease (n = 28, 43.1%), dysphagia (n = 20, 30.8%), recurrent respiratory infections (n = 23, 35.3%), chronic cough (n = 19, 29.2%), and pneumonia (n = 19, 29.2%). Tracheomalacia was diagnosed in 22(33.8%), 2 of whom required tracheostomy for severe disease. Overall mortality rate was 10.8% (n = 7): 5 demised due to chronic respiratory failure, while 2 demised intra-operatively during the index surgery. Conclusion Despite successful surgical repair for EA/TEF, our data demonstrated significant morbidities among EA/TEF survivors, thus highlighting the importance of long-term multi-disciplinary care with collaboration between respiratory, gastroenterology, and otolaryngology specialists. Level of evidence Prognostic, Level IV.