BACKGROUND AND STUDY AIM: Colonoscopy is a common gastroenterological procedure for investigation of the bowel. The main side effects of colonoscopy are pain during investigation, cardiovascular complications and very rarely even death. The aim of this study was to compare the continuous fluctuation of heart rate variability (HRV) components during colonoscopy under normal conditions, analgesia/sedation, and total intravenous anesthesia. PATIENTS AND METHODS: 37 consecutive patients (aged 35 - 65), were randomly allocated to three groups: no sedation (control group 1); analgesia/sedation (group 2); and total intravenous anesthesia (group 3). Holter electrocardiography and subsequent frequency domain analysis were undertaken. The low-frequency (LF, 0.04 - 0.15 Hz) and the high-frequency (HF, 0.15 - 0.40 Hz) components were estimated using spectral analysis in the usual way. Normalized units (nu) were calculated from the following equations: LFnu = LF/(LF + HF), and HFnu = HF/(LF + HF). RESULTS: Groups 2 and 3 were found to have a significantly lower HFnu and higher LFnu than group 1 essentially throughout the procedure. A one-way analysis of variance and t-test confirmed that the differences were significant when the colonoscope reached the splenic flexure as were the LF/HF balances at the splenic and hepatic flexures and the cecum. The percentage change in LF/HF was also analyzed, and it was found that in group 3 the mean change was over 136 % when the colonoscope reached the sigmoid flexure, which was significantly higher than in the other two groups. CONCLUSION: Most changes in HRV components occurred during colonoscopy of the left side of the bowel. Analgesia/sedation and total intravenous anesthesia increased HRV by increasing the LF component.