A 3-day-old, 2.2-kg former 34-week premature infant with imperforate anus required loop ileostomy surgery. At delivery, the child had respiratory distress. Endotracheal intubation was “confirmed” by detection of exhaled carbon dioxide with a Pedi-Cap (Covidien, Dublin, Ireland) and subsequent chest x-ray. On arrival to the operating room, the pulse oximeter reading was 100% despite a large leak around the endotracheal tube and high-airway pressures. Packing the throat reduced the leak and increased the tidal volume. Intraoperative bronchospasm occurred during the surgery. On postoperative day 1, fiberoptic examination by an otolaryngologist revealed esophageal intubation and the absence of laryngeal opening. Subsequent computed tomography scan revealed Floyd type II tracheal agenesis. To our knowledge, this is the only case of tracheal agenesis diagnosed after a non-airway related procedure. We discussed how the diagnosis was missed.