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Dexmedetomidine has been reported to have a renal protective effect after adult open heart surgery. The authors hypothesized that intraoperative infusion of dexmedetomidine would attenuate the decrease in renal function after pediatric open heart surgery.Twenty-nine pediatric patients (1–6 years) scheduled for atrial or ventricular septal defect repair were randomly assigned to receive either continuous infusion of normal saline (control group, n = 14) or dexmedetomidine (a bolus dose of 0.5 μg/kg and then an infusion of 0.5 μg/kg/h) (dexmedetomidine group, n = 15) from anesthesia induction to the end of cardiopulmonary bypass. Serum creatinine (Scr) was measured before surgery (T0), 10 minutes after anesthesia induction (T1), 5 minutes after cardiopulmonary bypass weaning (T2), 2 hours after T2 (T3), and after postoperative day 1 (POD1) and postoperative day 2 (POD2) and estimated glomerular filtration rates (eGFRs) were calculated. Renal biomarkers were measured at T1, T2, and T3. Acute kidney injury (AKI) was defined as an absolute increase in Scr of ≥ 0.3 mg/dL or a percent increase in Scr of ≥50%.The incidence of AKI during the perioperative period was significantly higher in the control group than in the dexmedetomidine group (64% [9/14] vs 27% [4/15], P = .042). eGFR was significantly lower in the control group than in the dexmedetomidine group at T2 (72.6 ± 15.1 vs 83.9 ± 13.5, P = .044) and T3 (73.4 ± 15.4 vs 86.7 ± 15.9, P = .03).Intraoperative infusion of dexmedetomidine may reduce the incidence of AKI and suppress post-bypass eGFR decline.