Background. Improvements in surgical techniques and perioperative management mean that more complex cardiac procedures are being performed on very young patients. Objectives. The aim of this study is to evaluate the effects of the duration of cardiopulmonary bypass (CPB) on renal injury after congenital heart surgery in infants and young children. Material and Methods. 58 children with ages <= 3 years undergoing CPB surgery were divided into three groups according to the duration of their CPB: Group I was < 90 min, n = 15; Group II, 90-149 min, n = 25; and Group III was >= 150 min, n = 18. Urinary neutrophil gelatinase-associated lipocalin, interleukin-18, microalbumin and alpha 1-microglobulin were measured at baseline and 4 h, 6 h, 12 h and 24 h after surgery. Results. No significant differences were noted among the groups in terms of gender, age, weight and baseline serum creatinine. The incidence of acute kidney injury (based on serum creatinine increase) after surgery were 13.3% (2/15) in Group I, 52.0% (13/25) in Group II and 77.8% (14/18) in Group III. 4 children developed acute renal failure (ARF) requiring peritoneal dialysis; all of them were in Group III. The levels of urinary biomarkers increased significantly, peaked at 4 h and remained elevated up to 24 h after surgery. Group III had significantly higher levels of urinary biomarkers than Groups I and II at 4-12 h after surgery, while the levels were not significantly different at 24 h. Conclusions. Prolonged CPB duration was related to more severe renal tubular injury and acute renal failure. Measurements of urinary kidney specific biomarkers in infants and children with a CPB duration of more than 150 min might help identify those at high risk for ARF