General anaesthesia is associated with a reduction in heart rate variability (HRV) compared to awake situation. In this study the hypothesis of reduction in HRV was tested in two different levels of anaesthesia depth. Forty six patients were randomly allocated in two groups, where anaesthesia was maintained with sevoflurane (n=23) or propofol (n=23). Administration of both anaesthetics was regulated in order to achieve a BIS value 25±5, followed by an increase to 55±5, both being stable for 5 min. HRV analysis included low frequency (LF), high frequency (HF) and total power (TP) measurements during the two levels of BIS. Estimated Normalized Values and LF/HF ratio were analyzed as well. Both logarithms of LF, HF and the Total Power values were changed in a statistically significant way from state of anaesthesia with BIS 25±5 to BIS 55±5 within each group of patients (0.24±0.53 vs 0.80±0.58, -0.73 ± 0.53 vs -0.17 ± 0.58, 5.16±5.49 vs 13.93±14.41 respectively for sevoflurane group, t-paired test p<0.05, 0.36±0.36 vs 0.76±0.43, -0.62 ± 0.35 vs -0.23 ± 0.36, 4.50±7.13 vs 10.40±14.38 respectively for propofol group, Wilcoxon test p<0.05). Normalized values and LF/HF ratios did not differ significantly, indicating similar sympathovagal balance between different levels of hypnosis. No difference between the two groups was found in terms of all HRV metrics with BIS values either 25±5 or 55±5. Conclusively, maintenance of anaesthesia with either propofol or sevoflurane affects HRV in a BIS dependent way without significant difference between them, but sympathovagal balance seems to remain unchanged.