Polycystic ovarian syndrome (PCOS) is a endocrine disorder characterized by irregular menstrual cycle, hyperandrogenism and polycystic ovaries. It is been reported that there is strong association between PCOS and cardio-metabolic risk. Cystatin C is non-glycosylated protein, acts as cysteine protease inhibitor and synthesized at a constant rate in all nucleated cells. Cystatin C are strongly associated with cardiovascular risk and correlated with changes inflammatory biomarkers and reliable marker for assessment of renal function. This study was to evaluate cystatin C levels in the PCOS cases and to correlate with BMI, Waist circumference and lipid levels. This cross-sectional study enrolled total of 108 women with PCOS and a group of 54 healthy volunteers as controls. Body mass index (BMI/kg m2) and waist circumference (cm) were measured and evaluated the Cystatin C and lipid levels in patients with PCOS and controls as well. Total cholesterol, triglyceride, LDL, and cystatin C levels were significantly higher and the HDL cholesterol levels were lower in comparison with healthy subjects (p < 0.05). We also found positive correlations between the cystatin C levels and BMI, Waist circumference, Total cholesterol and LDL levels in the PCOS patients. As PCOS is associated with higher levels of cystatin C and recent studies have suggested a role for cystatin C in progression of cardiovascular disease and its complications. More research and clinical studies are needed on the precise role of cystatin C as a cardiovascular risk factor in PCOS and measures to be taken to reduce the overall cardiovascular risk.