Neutrophil gelatinase-associated lipocalin (NGAL) has been implicated as an early predictive urinary biomarker of ischemic acute kidney injury (AKI). The aim of this study was to compare the effects of miniaturized cardiopulmonary bypass system (MCPB) vs. standard cardiopulmonary bypass system (SCPB) system on kidney tissue in patients undergoing myocardial revascularization using urinary NGAL levels as an early marker for renal injury. Sixty consecutive patients who underwent myocardial revascularization were studied prospectively. An SCPB was used in 30 patients (group A) and MCPB was used in 30 patients (group B). The SCPB group but not the MCPB group showed a significant NGAL concentration increase from preoperative during the 1st postoperative day (169.0±163.6 ng/ml in the SCPB group vs. 94.1±99.4 ng/ml in the MCPB group, P<0.05, respectively). Two patients in the SCPB group developed AKI and underwent renal replacement therapy; no patient in MCPB developed AKI. The MCPB system is safe in routine clinical use. Kidney function is better protected during MCPB as demonstrated by NGAL levels. NGAL represents an early biomarker of renal failure in patients undergoing cardiac surgery and the valuation of its concentration can aid in medical decision-making.