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Children undergoing congenital heart surgery require postoperative mechanical ventilation. Despite recent advances, prolonged mechanical ventilation (PMV) is necessary in some patients and may increase the risk of postoperative complications. The purpose of this study was to identify incidence and risk factors for PMV. The authors performed a retrospective chart review. They defined PMV as ventilation longer than 48 hours. Mixed-effects linear regression models were used to assess the relationship between each factor and duration of mechanical ventilation. Separate models were developed for preoperative, intraoperative, and postoperative periods. To determine the extent to which a combination of risk factors would predict PMV, the most significant variables were adopted to fit a model using number of risk factors to predict PMV. Two hundred twelve children ≤ 36 months were included. Eleven (5.2%) children died perioperatively. Of the patients, 72.6% (143/197) were extubated by 48 hours. Age < 6 months, perioperative infection, inotrope use > 48 hours, total parenteral nutrition use, and failed extubation were associated with PMV. PMV occurred in 28% of the patients in this study. The presence of 2 risk factors predicted PMV with a sensitivity of 86% and a specificity of 94%.