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Children who require prolonged intensive care after cardiac surgery are at risk of high mortality. The long-term survival and functional outcome of these children have not been studied in detail.Children who stayed in intensive care for >28 days after cardiac surgery from 1997 to 2012 were studied in a single institution. A total of 116 patients were identified; 107 (92%) were <1 year of age and 63 (54%) had univentricular physiology.The incidence of children requiring prolonged intensive care increased from 1.01/100 undergoing cardiac surgery in 1997 to 2000 to 2.66/100 in 2009 to 2012 (P trend = .002). This increase coincided with an increase in the number of children with hypoplastic left heart syndrome having prolonged intensive care during the same period (0.13/100 in 1997-2000 to 1.0/100 in 2009-2012; P trend = .001). Survival to pediatric intensive care unit (PICU) discharge was 74% (95% confidence interval [CI], 65-82) and 51% (95% CI, 41-59) at 3 years. Factors associated with mortality were univentricular repair (hazard ratio [HR], 2.12; 95% CI, 1.21-3.70; P = .008) and acute renal failure (HR, 3.01; 95% CI, 1.77-5.12; P < .001), but era did not influence mortality (1997-2005 vs 2006-2012; log-rank P = .66). Among PICU survivors, 3-year survival in those who did not need early reoperation was 81% (95% CI, 66-90), compared with 58% (95% CI, 42-71) in those who required early reoperation (log-rank P = .01). Among survivors, 36% had either moderate or severe disability and 13% had poor quality of life.The incidence of children requiring prolonged intensive care after cardiac surgery has increased in our institution. Our data suggest that the long-term outcome for most of these children is poor, especially after univentricular repair.