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We have investigated the effects of ketamine-based and remifentanil-based anesthetic protocol on perioperative serum cystatin-C levels, and creatinine and/or cystatin-C-based eGFR equations in terms of acute kidney injury in coronary artery bypass graft (CABG) surgery. Using a simple randomization method (coin tossing), patients were divided into the two groups and not-blinded to the anesthetist. Remifentanil-midazolam-propofol or ketamine-midazolam-propofol-based anesthetic regimen was chosen. Different eGFR formulas using creatinine (MDRD, CKD-EPI, Cockrauft Gault); cystatin-C (eGFR1, eGFR2) or a combination of creatinine and cystatin-C (eGFR 3) were used to calculate estimated glomerular filtration rates (eGFRs). High-sensitive troponin T was used to determine if ketamine use in coronary surgery contributed to myocardial cell damage. Thirty-seven patients were included in the study (remifentanil group = 19, ketamine Group = 18). Urea, creatinine, cystatin-C levels were comparable between the groups in all the measurement times and also postoperative day 2 samples showed statistically higher results compared to baseline (p < 0.001). Effects of ketamine and remifentanil on renal functions were found similar. Creatinine and cystatin-C-based eGFR equations resulted similar in our study. Reversible stage 1 acute kidney injury (AKI) was observed on postoperative day 2 in seven patients from the remifentanil group and six patients from the ketamine group. Hs-troponin T was found to be higher in postoperative day 1 samples; there were no significant difference between the groups. Our results indicated that patients who have normal renal functions undergoing on-pump coronary bypass surgery, effects of ketamine and remifentanil on renal functions in terms of AKI were found to be similar.