Background and objectives: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder seen in women of reproductive age and affecting 8-13% of them. In PCOS reduced HRV is due to weight gain, as obesity may deteriorate cardiac autonomic functions. Altered level of BDNF, a member of neurotrophin family, were observed in plasma and follicular fluid in women with PCOS. The aim of present study was to study the association of BDNF and HRV in PCOS. Methods: The present study involved180 women aged between 17 to 35 years with and without PCOS. Out of 180 women: 90 women with PCOS were enrolled as cases and 90 age-matched women without PCOS were enrolled as controls. Further, on the basis of BMI, study group was divided into two subgroups: Obese (OB) PCOS Group (BMI ≥25kg/m2 (n=50) and Non Obese (OB) PCOS Group (BMI ≤ 24.99) kg/m2 (n=40). Data was statistically analyzed using students unpaired t test and correlation between parameters was analyzed by Pearson’s rank correlation and p value <0.05 is considered significant. Results: HRV was significantly altered in women with PCOS in the form of increased sympathetic and decreased parasympathetic activity, especially in OB PCOS group. Additionally increased level of BDNF was observed but results were not statistically significant different.