Bispectral index (BIS) and monitoring of end-tidal concentration may be associated with a reduction in the incidence of awareness during volatile-based general anaesthesia. An analogue of end-tidal concentration during cardiopulmonary bypass (CPB) is measuring exhausted isoflurane concentration from the oxygenator as an estimate to blood and, so, brain concentration. The aim of this study was to determine the relationships between oxygenator exhaust and blood concentrations of isoflurane and the BIS score during CPB when administering isoflurane into the sweep gas supply to the oxygenator. Seventeen patients undergoing elective cardiac surgery using CPB and isoflurane with BIS monitoring were recruited in a single-centre university hospital. Isoflurane gas was delivered via a calibrated vaporiser at the beginning of anaesthetic induction. Radial arterial blood samples were collected after the initiation of CPB and before aortic cross-clamping, which were analysed for isoflurane by gas chromatography and mass spectrometry. The BIS score and the concentration of exhausted isoflurane from the oxygenator membrane, as measured by an anaesthetic gas analyser, were recorded at the time of blood sampling. The mean duration of anaesthetic induction to arterial blood sampling was 90 min (95%CI: 80,100). On CPB, the median BIS was 39 (range, 7-43) and the mean oxygenator exhaust isoflurane concentration was 1.24 ± 0.21%. No significant correlation was demonstrated between BIS with arterial isoflurane concentration (r=-0.19, p=0.47) or oxygenator exhaust isoflurane concentration (r=0.07, p=0.80). Mixed-venous blood temperature was moderately correlated to BIS (r=0.50, p=0.04). Oxygenator exhaust isoflurane concentration was moderately, positively correlated with its arterial concentration (r=0.64, p<0.01). In conclusion, in patients undergoing heart surgery with CPB, the findings of this study indicate that, whilst oxygenator exhaust concentrations were significantly associated with arterial concentrations of isoflurane, neither had any association with the BIS scores, whereas body temperature has moderate positive correlation.