OBJECTIVE: To compare the modulation of heart rate in a group of volunteers with polycystic ovary syndrome (PCOS) to that of a group of healthy ovulatory women on the basis of R-R interval variability and analyze the relationships between heart rate variability (HRV) and other cardiovascular risk factors. METHODS: In a cross-sectional study, HRV and anthropometric, biochemical and hormonal parameters were measured in 23 women with PCOS and 23 age-matched controls. Mean outcomes measures: HRV indexes in the time (SDNN and rMSSD) and frequency domain (low frequency-LF and high frequency-HF). Differences between groups and correlation analysis were performed. RESULTS: Intergroup analysis showed significant differences (p < 0.05) between groups, with lower SDNN, rMSSD, LF and HF indexes in PCOS women when compared to the control group. There was significant negative correlation between BMI and SDNN, LF and HF, indicating a decrease in the autonomic modulation of heart rate with increasing weight. A negative correlation was also found between the high-sensitivity C-reactive protein level and the rMSSD index. CONCLUSION: Our results show that PCOS is associated with alterations in the autonomic modulation of heart rate, possibly due to the influence of weight gain.