We aimed to determine the independent predictors of cardiovascular risk in polycystic ovarian syndrome (PCOS). Ninety-one PCOS and 51 control patients were enrolled to our prospective cross sectional case-control study. In early follicular phase hormonal and lipid profile, fasting insulin and CRP (hs-CRP) levels and glucose levels on fasting and 2 h after the 75 g glucose intake were determined. Insulin resistance (IR) was evaluated with homeostasis model assessment and free testosterone was determined with free androgen index. PCOS was found to be associated with dyslipidemia, hyperandrogenism, IR and sub-clinical inflammation. The prevalence of overweight-obesity (41.8% vs. 25.5%, p = 0.038), IR (42.9% vs. 23.5%, p = 0.035) and glucose intolerance (15.38% vs. 1.96%, p = 0.043) were significantly higher in PCOS compared to control group. Independent predictors of the risk of elevated hs-CRP level were PCOS status (OR = 5, 95% CI: 1.55-16.14, p = 0.007) and high BMI (OR = 4.2, 95% CI: 1.2-14.2, p = 0.022) and high BMI (OR = 1.2, 95% CI: 1.05-1.4, p = 0.007) and of TC/HDL ratio was high BMI (OR = 1.21, 95% CI: 1.05-1.4, p = 0.009) and increasing age (OR = 1.11, 95% CI: 1.01-1.2, p = 0.04). The presence of PCOS, independent from obesity and IR, is the strongest predictor of elevated hs-CRP level. Obesity and advanced age further increases the cardiovascular risk in PCOS.