To evaluate the safety and efficacy of prolonged dexmedetomidine administration (≥ 96 hrs) in critically ill children with heart disease. Retrospective observational study. Cardiovascular intensive care unit in a single, tertiary care, academic children's hospital. None. We conducted a retrospective review of the charts of all critically ill infants and children (up to 18 yrs of age) with congenital or acquired heart disease who received dexmedetomidine for ≥ 96 hrs in our pediatric cardiovascular intensive care unit between January 2009 and March 2010. Patients were divided into two groups for study purposes: the dexmedetomidine group (n = 52) included patients who received a dexmedetomidine infusion along with other conventional sedation agents, and the control group (n = 42) included patients who received conventional sedation agents without the use of dexmedetomidine. Clinical outcomes evaluated in our study included days of mechanical ventilation, cardiovascular intensive care unit length of stay, hospital length of stay, and mortality. To evaluate the safety of dexmedetomidine, we collected physiologic data, including heart rate, mean arterial pressure, respiratory rate, systemic oxygen saturation by pulse oximetry, and inotrope score. To assess the efficacy of dexmedetomidine, we examined the amount and duration of concomitant sedation and analgesic infusions over a period of 24 hrs in both dexmedetomidine and control groups. We also examined the number of rescue boluses for each category prior to the initiation of sedative infusion, during the sedative infusion, and after the termination of the sedative infusion. The potential side effects evaluated in our study included nausea, vomiting, abdominal distension, dysrhythmias, neurological abnormalities, seizures, and signs and symptoms of withdrawal. Patients' baseline characteristics were similar in the two groups. Patient complexity as measured by Risk-Adjusted Classification for Congenital Heart Surgery-1 score, ventricular ejection fraction, and proportion of patients receiving mechanical ventilatory support at the time of initiation of sedative infusion was also similar. The duration and amount of continuous midazolam and morphine infusions were significantly lower in the dexmedetomidine group when compared to the control group. During dexmedetomidine infusion, there was no statistical difference in the heart rate and blood pressure between the two groups. Inotrope score was significantly lower in the dexmedetomidine group as compared to the control group in the last 6 hrs prior to termination of dexmedetomidine infusion (p < .001), and at 1 hr (p < .001) and 6 hrs (p < .001) after termination of dexmedetomidine infusion. There was no difference in duration of mechanical ventilation (p = .77), cardiovascular intensive care unit length of stay (p = .29), or hospital length of stay (p = .43) in the two groups. One patient experienced junctional rhythm at 130 beats/min requiring temporary pacing. No other significant side effects were noted. A higher proportion of patients in the dexmedetomidine group were administered clonidine when compared to the control group after termination of dexmedetomidine (31% vs. 7%, p = .005). Prolonged dexmedetomidine administration in children with heart disease appears to be safe and is associated with decreased opioid and benzodiazepine requirement and decreased inotropic support.