Objective: To assess risk factors of acute kidney injury in congenital cardiac disease following cardiac surgery with cardiopulmonary bypass in children. Mathods: A 50% postoperative creatinine increase was regarded as the criterion of acute kidney injury. 124 children aged 3 years or little undergoing cardiac surgery were divided into three groups: (1) negative AKI (-); (2) AKI (+) with an increase in postoperative creatinine from 150% to 200%; and (3) AKI (++) with an increase in postoperative creatinine by more than 200%. Demographics, and preoperative, intraoperative, and postoperative variables were evaluated for associations with AKI using univariate and multiple logistic regression analysis. Results: Several variables, including mortality, preoperative albumin and creatinine levels, cardiopulmonary bypass duration, and postoperative creatinine levels, were significant differences among the three groups (P < 0.05). Multiple regression analysis demonstrated that three risk factors, age (OR, 0.962; 95% CI, 0.925 to 1.000; P = 0.046), intraoperative red blood cell transfusion (OR, 1.003; 95% CI, 1.001 to 1.005; P = 0.030), and cardiopulmonary bypass duration (OR, 1.024; 95% CI, 1.016 to 1.032; P = 0.000) were independently associated with AKI after cardiac surgery. Conclusions: This study showed that younger age, incremental intraoperative red blood cell transfusion, and prolonged cardiopulmonary bypass duration were independently associated with acute kidney injury after cardiac surgery. The type of congenital cardiac disease should be included in the analysis of acute kidney injury.