Introduction This study compared the effect on renal function of flucloxacillin and vancomycin antibiotic prophylaxis for elective first-time coronary artery bypass grafting (CABG) surgery, using both direct biochemical markers and indirect clinical outcome measures. Recent evidence has suggested that vancomycin may be nephrotoxic in patients undergoing cardiac surgery. Methods A retrospective observational study of patients undergoing elective first-time CABG was performed, covering a 13-month period. All patients received prophylactic antibiotics: flucloxacillin 1 g pre-operatively and three 1 g doses post-operatively. Patients who were MRSA-positive, MRSA unknown or penicillin allergic received an alternative regimen: vancomycin 1 g pre-operatively and 1 g post-operatively. Exclusion criteria: pre-operative creatinine >133 mmol/l, any antibiotics other than prophylaxis and haemodynamic support except <5 μg/kg/hour dopamine. Results Of 1,413 patients in the study period, 415 met the study criteria: 360 patients received flucloxacillin and 55 patients received vancomycin. There were no significant differences between the two groups in sex, age, BMI, euroSCORE, diabetes status, ejection fraction, pre-operative creatinine, eGFR, sodium, or potassium. Comparing change in renal function pre-operatively to post-operatively, there were no significant group differences in change in: creatinine (mmol/l; VAN median 0 (IQR 11); FLU -2 (19); P = 0.22), eGFR (ml/min; VAN 0 (14); FLU 2.4 (19.3); P = 0.22), sodium (mmol/l; VAN 1 (4); FLU 1 (4); P = 0.28). Change in potassium differed significantly (mmol/l; VAN 0.7 (0.9); FLU 0.5 (0.7); P < 0.05). In clinical outcome measures, the groups were similar. Most patients in both groups stayed in ITU for 1 day and there was no significant difference in the number of patients staying for longer than 1 day (VAN 7/55 (13%); FLU 29/360 (8%); P = 0.30). There was no difference in hospital length of stay (days; VAN 7 (4); FLU 6 (3); P = 0.19). Conclusions In elective first-time CABG patients, there is no significant difference in change in renal function between those given vancomycin antibiotic prophylaxis and those given flucloxacillin prophylaxis, as assessed by creatinine, eGFR and sodium levels, and indirect clinical outcome measures. Potassium increased more in the vancomycin group but the clinical significance of this is unclear. Our data suggest that prophylactic vancomycin does not impair renal function relative to flucloxacillin.