Background: Polycystic ovarian syndrome and obesity contribute to the metabolic problems that reproductiveage women experience. Objective: This research aimed to examine the effect of abdominal obesity using BMI and the waist/hip ratio [WHR] on metabolic parameters in patients with polycystic ovary syndrome. Patients and Methods: This prospective study was carried out on eighty [80] women, aged 20- 35 years-old attending the Gynecology Clinic of Zagazig and Al-Ahrar Educational Hospital. The selected cases were divided into four groups after taking a written or verbal consent to be included in the study: Group I: Twenty cases of obese PCOS, Group II: Twenty cases of non-obese PCOS, Group III: Twenty cases of obese non-PCOS and Group IV: Twenty cases of non-obese non- PCOS. Results: Lipid profile in obese PCOS and non obese PCOS demonstrated statistically highly significant difference between both groups regarding serum total cholesterol, serum triglycerides and serum low density lipoprotein [LDL]. There was a statistically insignificant differences between both groups as regard serum very low density lipoprotein [VLDL]. Conclusions: This study showed that women with PCOS had atherogenic lipoprotein profile characterized by increased cholesterol, LDL and triglycerides especially in obese group, which might be a risk factor for developing cardiovascular complication.