The aim of this study was to evaluate the effects of combination psychotropic drug treatment on heart rate variability (HRV), which was mainly controlled by the parasympathetic nervous system. Mean R-R intervals (mRR) and coefficient of variation (CV), an index of HRV, were studied in 22 psychiatric patients and 21 age- and sex-matched healthy controls. Next, in the patient group focusing on both anticholinergic and antidopaminergic properties, combination psychotropic drug daily doses were converted into biperiden milligram equivalents (BPDeq) and chlorpromazine milligram equivalents (CPZeq), respectively. The relationship between mRR and CV and these equivalent dosages was examined. A significant reduction in both mRR (P < 0.05) and CV (P < 0.05) was found in the patient group. In addition, significant negative correlations were observed between the dose of BPDeq and mRR (P < 0.05), and between the dose of BPDeq and CV (P < 0.005). In contrast, no significant correlations were observed between the dose of CPZeq and either parameter. These findings suggest that the effects of combination psychotropic drug treatment on HRV are mainly due to their anticholinergic properties. Therefore, CV is a useful indicator to assess the parasympathetic activity of psychiatric patients under combination psychotropic drug treatment.