Perinatal pharyngoesophageal instrumentation, including endotracheal intubation, oral suctioning, and feeding tube placement, is often necessary but risks tissue damage. Our objective was to estimate the incidence of iatrogenic perinatal pharyngoesophageal injury (IPPI) in preterm versus term infants in a children's hospital neonatal intensive care unit (NICU). A secondary goal was to explore the clinical characteristics and outcomes associated with these complications.All NICU discharge summaries from 2004 to 2008 were searched for IPPI-related keywords. Highlighted records were reviewed and the incidence of complications calculated by gestational age and weight.Of 5910 total NICU discharges, 6 cases of IPPI were identified, for an overall incidence of 0.10%. All injuries occurred in infants less than 33 weeks gestational age and 1500g, with a trend towards higher incidence with increasing prematurity. The incidence of IPPI rose to 4/1321 (0.30%) at 27–32 weeks and 2/521 (0.38%) at less than 27 weeks gestation. Similarly, IPPI occurred in 3/675 (0.44%) babies born at 1000–1500g and 3/642 (0.47%) babies below 1000g. All affected infants survived with conservative management.IPPI is a rare but serious complication of perinatal airway instrumentation and is primarily a disease of prematurity. In this sizeable cohort, no complications occurred in term infants, and the incidence of injury increased with decreasing gestational age and weight. This increased propensity towards injury should prompt special care when performing even routine airway procedures on premature neonates.