Polycystic ovary syndrome (PCOS) is associated with cardiovascular risks like obesity, insulin resistance, dyslipidemia that can lead to sympathovagal imbalance (SVI). The study was designed to assess the cardiovascular risk in PCOS and link of metabolic derangements to SVI. Thirty-five newly diagnosed PCOS patients and 32 age-matched controls were recruited. Waist-hip ratio, body mass index (BMI), basal cardiovascular parameters such as basal heart rate (BHR), systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP) and rate pressure product (RPP) were recorded. Autonomic functions were assessed using short-term heart rate variability (HRV) analysis, heart rate and blood pressure response to standing (30:15 ratio), deep breathing (E:I ratio) and isometric handgrip (DeltaDBPihg). Fasting plasma glucose, insulin, lipid profile and testosterone were assayed. Insulin resistance (HOMA-IR) and lipid risk factors were calculated. The cases had increased BHR, BMI, SBP, DBP, MAP and RPP. The ratio of low-frequency to high-frequency (LF-HF) of HRV, the marker of SVI was significantly increased in cases. 30:15 ratio and DeltaDBPihg were increased and E:I ratio was decreased in the cases. HOMA-IR, lipid risk factors and testosterone were significantly elevated in cases. There was a significant correlation of LF-HF with BMI, BHR, RPP, insulin resistance and lipid risk factors. On regression analysis, insulin resistance and lipid risk factors had independent association with LF-HF. PCOS patients have SVI, decreased HRV and increased RPP and the potential cardiovascular risks. The insulin resistance and dyslipidemia contribute to SVI and cardiovascular risks in PCOS patients.