Objectives PCOS is the most common endocrinological disorder amongst women of reproductive age. The consequences of PCOS extend beyond the reproductive axis and may lead to the development of metabolic syndrome leading to a high risk for hypertension and cardiovascular disease. Therefore, a more comprehensive evaluation of biochemical markers that reflect the cardiovascular risk is required for further understanding of pathophysiologic mechanisms, diagnosis and management. Methods In this case-control study, women diagnosed with PCOS (n=100) in the age group (18–35 years) years were taken as cases and age matched healthy controls (n=100) were enrolled. Estimations of fasting plasma Glucose, serum total cholesterol (TC), triglycerides (TG) and High-density lipoprotein (HDL) concentrations were assayed while Low-density lipoprotein (LDL) was calculated by using Fredrickson Friedwald’s formula. Serum Lipoprotein-a (Lp-a) was estimated using ELISA (Enzyme Linked Immunosorbent Assay). The quantitative data were expressed as Mean ± Standard Deviation (SD). Unpaired Student’s t-test was used to compare the values (PCOS vs Controls) and Pearson’s correlation coefficient was used to elucidate the relationship between the variables. Results FBS and all lipid parameters were significantly increased in PCOS patients compared to control subjects. On the other hand, HDL-C was significantly decreased as compared to the control subjects. The hormones TSH, LH, FSH, PRL and LH/FSH ratio were significantly increased in PCOS patients compared to control subjects. Lipoprotein-a and PAI-1 was significantly increased in PCOS patients compared to the control subjects. Upon bivariate correlation analysis, Lp(a) had significant correlations with PAI-1 (r=0.35, p=0.000), WHR (r=0.25, p=0.000), LDL (r=0.52, p=0.000) and TSH (r=0.24, p=0.000). While the correlations with FBS (r=−0.008, p=0.91) and LH/FSH ratio (r=−0.004, p=0.95) were statistically insignificant. Conclusions The evaluation of serum biomarkers such as Lp-a, PAI-1 and lipid profile routinely in PCOS patients may have diagnostic role in the early detection of metabolic abnormalities and endocrine derangements and timely management of comorbid Diabetes and Cardiovascular disease in PCOS females.