Rationale: Tracheobronchomalacia is a common comorbidity in neonates with bronchopulmonary dysplasia. However, the effect of tracheobronchomalacia on the clinical course of bronchopulmonary dysplasia is not well-understood. Objective: We sought to assess the impact of tracheobronchomalacia on outcomes in neonates with bronchopulmonary dysplasia in a large, multi-center cohort. Methods: We preformed a cohort study of 974 neonates with bronchopulmonary dysplasia admitted to 27 neonatal intensive care units participating in the Children's Hospital Neonatal Database who had undergone bronchoscopy. In hospital morbidity for neonates with bronchopulmonary dysplasia and tracheobronchomalacia (N=353, 36.2%) was compared to those without tracheobronchomalacia (N=621, 63.8%) using mixed-effects multivariate regression. Results: Neonates with tracheobronchomalacia and bronchopulmonary dysplasia had more comorbidities, such as gastroesophageal reflux (OR=1.65, 95%CI 1.23- 2.29, P=0.001) and pneumonia (OR=1.68, 95%CI 1.21-2.33, P=0.002) and more commonly required surgeries such as tracheostomy (OR=1.55, 95%CI 1.15-2.11, P=0.005) and gastrostomy (OR=1.38, 95%CI 1.03-1.85, P=0.03) compared with those without tracheobronchomalacia. Neonates with tracheobronchomalacia were hospitalitized (118 ± 93 vs 105 ± 83 days, P=0.02) and ventilated (83.1 ± 91.1 vs 67.2 ± 71.9 days, P=0.003) longer than those without tracheobronchomalacia. Upon discharge, neonates with tracheobronchomalacia and BPD were more likely to be mechanically ventilated (OR=1.37, 95CI 1.01-1.87 P=0.045) and possibly less likely to receive oral nutrition (OR=0.69, 95%CI 0.47-1.01, P=0.058). Conclusions: Tracheobronchomalacia is common in neonates with bronchopulmonary dysplasia who undergo bronchoscopy and is associated with longer and more complicated hospitalizations.