Tracheomalacia is associated with esophageal atresia (EA), but may go unnoticed from external splinting forces. Intra-operative dissection with fistula division releases external splinting, revealing tracheomalacia only post-operatively. Analysis of surgical technique may disclose an iatrogenic etiology. From 1995 - 2004, 44 neonates underwent surgery for EA. All patients underwent pre-, intra- and postoperative bronchoscopy. Operative and bronchoscopic notes were studied for malacia, and extensive dissection of the esophagus and fistula from the trachea. Surgical mortality was 6.8 %. Pre-operative tracheomalacia was diagnosed in 3 patients, who eventually fared well. In 17 other patients, the pre-operative bronchoscopy was negative, but airway obstruction developed post-operatively. Tracheomalacia was documented at the site of the former fistula and surgical release maneuvers. Aortopexy was required in 5 instances, whereas 12 others with malacia were managed conservatively. Mediastinal connective tissue and the fistula may splint open the marginally diseased airway in patients with EA, the lack of which may disclose previously unknown tracheomalacia after repair. When aggressive release maneuvers have been required, early aortopexy may be preferred to ventilator dependency.