Objective: Early extubation in the operating room after surgery for congenital heart disease has been described; however, postoperative mechanical ventilation in the intensive care unit remains common practice in many institutions. The goal of this study was to identify perioperative factors associated with not proceeding with planned operating room extubation. Methods: We performed a retrospective chart review of 224 patients (aged 1 month to 18 years, median 20 months) undergoing surgery for congenital heart defects requiring cardiopulmonary bypass. Patients mechanically ventilated preoperatively were excluded. A stepwise logistic regression model was used to test for the independent influence of various perioperative factors on extubation in the operating room. Results: Overall, 79% of patients were extubated in the operating room. Younger age and longer cardiopulmonary bypass time were the strongest predictors for not extubating. Each step down to a younger age group (<2, 2-4, 4-6, 6-12, >12 months) reduced the chance of extubation in the operating room by 56%. Cardiopulmonary bypass time for more than 150 minutes was associated with an 11.8-fold increased risk of not being extubated. Male gender and high inotrope requirement after cardiopulmonary bypass were also significantly associated with fewer children being extubated. Conclusion: Extubation in the operating room after surgery for congenital heart disease was successful in the majority of patients. The strongest independent risk factors for failure of this strategy included younger age and longer cardiopulmonary bypass time.