BACKGROUND: Limited data are available related to the effects of sex hormones on cardiac autonomic function. Few studies investigated the heart rate variability (HRV) parameters during regular menstrual cycle or in postmenopausal women using hormone replacement therapy, but the results were contradictory. The aim of the study was to compare the characteristics of the autonomic innervation of the heart in polycystic ovary syndrome (PCOS) patients with regularly cycling controls. METHODS: Thirty PCOS patients and 30 healthy regularly cycling controls were included in the study. Groups were compared with respect to age and various cardiovascular risk factors. Characteristics of autonomic innervation of the heart were evaluated with HRV. Power spectral analysis of HRV was performed to calculate the low frequency peak (LF 0.04-0.15 Hz), high-frequency peak (HF 0.15-0.40 Hz), LF in normalized unit (LF nu), HF in normalized unit (HF nu) and LF/HF ratio. RESULTS: PCOS patients had adverse cardiovascular risk profile than controls. As the HRV parameters, PCOS patients had significantly higher LF nu (P = 0.005) and LF/HF ratio (P = 0.001) and significantly lower HF (P = 0.006) and HF nu (P < 0.001) compared to controls. CONCLUSION: Autonomic innervation of the heart can be affected in PCOS with increased sympathetic and decreased parasympathetic components of HRV. As a result, sympathetic to parasympathetic ratio may increase in PCOS. This finding should be confirmed with larger studies also evaluating the clinical implications of altered HRV parameters.