Vitamin D deficiency is commonly encountered in obese women in the reproductive age group. Low levels of vitamin D has been linked to insulin resistance which may affect the reproductive and endocrine functions of the ovaries and may also increase the risk of several metabolic disturbances in women with polycystic ovarian syndrome (PCOS). We conducted a retrospective cross sectional analysis of 70 women (15-50 years) with PCOS to determine whether vitamin D (25(OH)D) levels have any impact on their clinical or biochemical parameters. These women were diagnosed as per Rotterdam criteria and their clinical, anthropometric and biochemical parameters were compared with age-matched controls. Women with PCOS had higher BMI (p < 0.0001), systolic (p = 0.0003) and diastolic (p = 0.02) blood pressure, low HDL (p < 0.0001) and low mean average 25(OH)D levels (27.3 ± 14.1 vs. 46.3 ± 19.3 nmol/L; p < 0.0001). Vitamin D deficiency was more prevalent in PCOS women (58.6% vs. 22.9%; p < 0.0001) whereas vitamin D insufficiency was higher in the control group (40.0% vs. 34.3%; p = 0.48). Low 25(OH)D was mostly noted in PCOS women who were either overweight or obese and a negative correlation existed between BMI and 25(OH)D (r = -0.83; p = 0.71). Biochemical parameters didn’t differ as per 25(OH)D status in PCOS women but an inverse relationship existed between 25(OH)D with DHEAS (p = 0.0004) and Androstenedione (p = 0.02) levels. 10% of PCOS women had metabolic syndrome (MetS) but 25(OH)D levels didn’t differ in women with or without MetS (p = 0.44). Logistic regression analysis didn’t show any association between MetS and 25(OH)D (OR: 1.004, 95% CI 0.949-1.061; p = 0.88). In conclusion, vitamin D deficiency is common in women with PCOS. Obesity not only influences development of PCOS but also determines vitamin D levels in these patients. Vitamin D does not influence clinical or metabolic parameters in PCOS but may affect circulating androgen levels.