Background: There are few data on the effects of anesthesia and cardiopulmonary bypass (CPB) on perioperative renal function in children with cyanotic congenital heart disease undergoing open heart surgery. This study aims to investigate the perioperative renal function in cyanotic versus acyanotic children undergoing sevoflurane anesthesia for open heart surgery. Methods: After receiving ethical committee approval, 12 acyanotic patients (preoperative oxygen saturation: SaO(2) > 85%) and 12 cyanotic children (SaO(2) < 85%) were included. Sevoflurane was administered at concentration levels of 2% before CPB and 1-2% during CPB after standard anesthesia induction. Inorganic fluoride, electrolytes, creatinine, urea nitrogen in serum and urine samples, and N-acetyl-beta-D-glucosaminidase (NAG) in urine samples were measured before induction, before CPB, during CPB, after CPB, at the end of surgery, and at 24th h postoperatively. Results: The levels of serum uric acid levels were higher in the cyanotic group (p < 0.05). There were no differences in the levels of serum creatinine and urine creatinine, urea nitrogen, and electrolytes between the two groups. Serum inorganic fluoride levels were always higher in the acyanotic group than in the cyanotic group, but these differences between the groups reached statistical significance at two measurement times (before CPB and end of surgery) (p < 0.05). Urinary inorganic fluoride levels increased with time in both groups. Although urinary NAG increased significantly after the CPB in the cyanotic group, the differences between the two groups did not reach statistical significance. Conclusions: We have concluded that renal function was not affected during open heart surgery with sevoflurane anesthesia, in both cyanotic and acyanotic children.