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This study aimed to evaluate adverse cardiac events using dexmedetomidine in infants with trisomy 21 and those without (controls) and examined potential risk factors in infants after cardiovascular surgery. We conducted a single-center retrospective cohort study. The medical records of 124 consecutive infants who had undergone cardiovascular surgery between April 1, 2013, and October 31, 2015, were enrolled. Clinical characteristics, usage of dexmedetomidine, and perioperative medications were analyzed. Adverse cardiac events were assessed with the Naranjo score and World Health Organization-The Uppsala Monitoring Centre (WHO-UMC) criteria. In total, 124 consecutive infants (30 patients and 94 controls) met the inclusion criteria. Eight of 30 (26.7 %) patients with trisomy 21 and 12 of 94 (12.8 %) controls experienced adverse cardiac events (i.e., hypotension, transient hypertension, and bradycardia) during dexmedetomidine with median Naranjo score of 6, and causality categories of WHO-UMC criteria were "certain" or "probable." Of those, the incidence of bradycardia occurred at a higher rate in patients with trisomy 21 than in controls (P = 0.011). Multiple logistic regression analysis revealed that the presence of trisomy 21 was an independent risk factor for adverse cardiac events of dexmedetomidine after cardiovascular surgery (odds ratio 4.10, 95 % CI 1.17-11.19, P = 0.006). Dexmedetomidine is associated with an increased incidence of bradycardia in patients with trisomy 21 after surgery for congenital heart disease. Physicians using dexmedetomidine should know a great deal about the characteristics of patients with trisomy 21, and hemodynamic monitoring should be closely observed.