We undertook this study to evaluate the effects of needle acupuncture on cardiac autonomic nervous system (ANS) function in patients with minor depression or anxiety disorder. Patients (n = 36) were randomly distributed into a verum acupuncture (VA) group (needles were applied at classical acupuncture points, e. g. He7, Pe6, Du20, Bl62, Ex6) or a placebo (PL) group (needles were applied only epidermal at non-acupuncture points). Both groups underwent standardized measurements of the 5-minute resting heart rate variability (HRV), which were performed before the first and after the 9th acupuncture session of an acupuncture series, and also three times (before the start and 5, respectively, 15 minutes after needle application) during the third acupuncture session. Demographic data between the VA and PL group did not differ. Before the start of acupuncture there were also no significant differences in HRV data between these groups. Compared to PL the VA group showed a significant decrease of the mean resting heart rate both, 5 and 15 minutes after needle application, combined with a trend towards an increase of the high frequency (HF; 0.15 - 0.4 Hz) and a decrease of the low frequency (LF; 0.04 - 0.15 Hz) spectral power. The latter effects resulted in an overall significant decrease of the mean LF/HF ratio in VA compared to PL treated patients. This pattern of findings suggests that in patients with minor depression or anxiety only verum acupuncture 1.) leads to a relative increase of cardiovagal modulation of heart rate and 2.) facilitates the physiological regulatory ANS function in response to alterations of external or internal environment. Clinical implications of these findings are discussed.