During anaesthesia awareness and nociception are serious complications that may further lead to haemodynamic instability. Specific monitoring of depth of hypnosis and depth of analgesia based on heart rate variability (HRV) analysis is eligible to improve patient safety and reduce efforts in post-operative care. Consequently, in this analysis we assess the applicability of HRV parameters during surgical interventions with standardized intravenous propofol-remifentanil-anaesthesia. Peri-operative electrocardiograms were recorded from cardiovascular stable patients (ASA Score I II, N = 32, age: 36.4 ± 11.23 a, BMI: 25.2 ± 3.16) scheduled for trauma and dentofacial surgery. HRV time- and frequency-domain parameters, measures of complexity and nonlinear dynamics were compared by analysing longitudinally distributed 300 s intervals preceding/following induction of anaesthesia (BL-I1), intubation (I1-I2) and extubation (E1-E2). Mean value (meanNN) and standard deviation (sdNN) of the heart rate are influenced in BL-I1 (p < 0.001), I1-I2 (p < 0.05) and E1-E2 (p < 0.001). The number of forbidden words of symbolic dynamics changes significantly for BL-I1 (p < 0.001) and not for I1-I2 and E1-E2 (p > 0.05). Probability of low-variability POLVAR10 is significantly altered in all comparisons (BL-I1: Δ = 0.032, p < 0.01, I1-I2: Δ = 0.12, p < 0.05, E1-E2: Δ = 0.169, p < 0.01) but especially during nociception. While standard time-domain parameters lacked selectivity, parameters of symbolic dynamics appear to be specifically influenced by changes in depth of hypnosis and nociception, respectively. However, the lack of steady-state ventilation/breathing in this study needs to be considered in future research. To be used for clinical anaesthesia monitoring our results have to be prospectively validated in clinical studies.