Purpose: The aim of the study was to compare the characteristics of the autonomic innervation of the heart in polycystic ovary syndrome(PCOS) patients with regulary cycling controls. Methods: We studied 21 patients visiting $igcircigcirc$hospital from 25th June 2009 to 25th June 2010. The subjects were categorized in two groups, 11 PCOS patients and 10 healthy regularly cycling controls. We studied the difference of Heart rate variability (HRV) between two groups by Independent samples T-test using SPSS for windows(version 17.0). Results: The Standard deviation of all normal R-R intervals (SDNN), The spuare root of the sum of the spuare of difference between adjacent normal R-R intervals (RMS-SD) of PCOS group was non-significantly lower than non-PCOS group. High frequency power (HF) and Normalized high frequency power (HF norm) of PCOS group was significantly higher than non-PCOS group. Normalized low frequency power (LF norm) of PCOS was signficantly lower than non-PCOS group. The results means increased sympathetic and decreased vagal modulation. Total power (TP), Very low frequency power (VLF) of PCOS group was non-significantly lower than non-PCOS group. Low frequency power (LF), LF/HF ratio of PCOS group was non-significantly higher than non-PCOS group. Conclusion: The results suggest that PCOS can be related to decreased activity of parasympathetic nervous system.