Introduction: The diagnosis of trisomy 21 in children has been associated with failed extubation after CHD surgery. Dexmedetomidine may be a useful agent to improve postoperative outcomes in these patients, such as ventilator time, ICU length of stay, or hospital length of stay. Materials and methods: The Pediatric Health Information System database was queried from January, 2008 to December, 2010 for patients with trisomy 21 who underwent CHD surgery. Patients who received dexmedetomidine were matched to patients who did not by propensity score. The primary outcome was ventilator days charged, and secondary outcomes included ICU and hospital length of stay. Results: A total of 1088 patients (544 matched pairs) met inclusion criteria. Patient characteristics were similar, with the exception of more patients in the dexmedetomidine group undergoing repair of complete atrioventricular canal and fewer undergoing mechanical valve replacement (p<0.01). More patients in the dexmedetomidine group were administered milrinone, epinephrine, vasopressin, benzodiazepines, opiates, and adjunct pain and sedative medications (p<0.01). The dexmedetomidine group had greater time on the ventilator [7 (4.5–11) versus 6 (4–10) days (median, interquartile range) p<0.01] and similar ICU length of stay, hospital length of stay, and mortality compared with controls. Mixed-effects modelling clustered on institution did not show beneficial effect of dexmedetomidine on ventilator time, ICU stay, or hospital length of stay. Conclusions: The use of dexmedetomidine was not associated with the decreased ventilatory time. Routine use of dexmedetomidine is not warranted in this patient population.