Acute kidney injury (AKI) is a serious complication in the perioperative period and is consistently associated with increased morbidity and case fatality rate. This has been best studied in the cardiac surgery setting where it has been shown that up to 11.5–86.0% of patients exposed to cardiopulmonary bypass (CPB) will develop AKI, with 2.0–18.9% requiring renal replacement therapy (RRT). A prospective uncontrolled cohort study was conducted between 2011 and 2015, in which 93 children with various congenital heart lesions undergoing CPB were enrolled. Serum creatinine (SCr) level was determined by Jaffé’s method (Cobas 6000 analyser, Roche). Postoperative fluid balance was estimated as the difference between fluid intake and output. Data for further processing were retrieved from anaesthesia and intensive care data management system flowsheets (IntelliView, Philips). AKI developed in 42 patients (45.6%) by meeting at least KDIGO (Kidney Disease: Improving Global Outcomes) stage I criteria (with SCr rise by more than 50% from the baseline). Thirty eight patients complied with the 1st stage of AKI, three with 2nd stage and two with 3rd stage, according the KDIGO classification and staging system. One patient having severity stage II and two patients having severity stage III of AKI required initiation of RRT using peritoneal dialysis. Two patients from the RRT group survived, one died. The median intraoperative urine output was 2.32 ml/kg/h, (range from 0.42–5.87 ml/kg/h). Median CPB time was 163 min., median aortic cross-clamping time was 97.9 min., cooling during CPB to 29.5 °C. The diagnosis of AKI using SCr was delayed by 48 hours after CPB. Median fluid balance (FB) on the first postoperative day in non-AKI patients was 13.58 ml/kg (IQR 0–37.02) vs 49.38 ml/kg (IQR 13.20–69.32) in AKI patients, p < 0.001. AKI is a frequent complication after open heart surgery in children with congenital heart lesions. From 93 patients included in the study, 42 (45.2%) met at least KDIGO Stage I criteria for AKI. FB is a sensitive marker of kidney dysfunction. Median FB in the 1st postoperative day significantly differed between AKI patients: 49.38 ml/kg (13.20–69.32) versus 13.58 ml/kg in patients with intact kidney function (AUC = 0.84; p = 0.001). Thus it can be used as a marker of AKI.