Background: Polycystic ovary syndrome (PCOS) is a common reproductive endocrine disorder associated with cardiovascular disease (CVD) risk factors and metabolic disturbances and a genetically heterogeneous disease. Intima-media thickness (IMT) is an indicator of atherosclerosis. This study aimed to determine the relation between IMT and PCOS in women. Methods: This cross-sectional study was performed on 44 PCOS patients and 44 healthy women. Data collection included lipid profiles, blood pressure, waist circumference, body mass index (BMI), and common and internal IMT of carotid artery which were measured in studied subjects. IMT was measured by a radiologist using a linear 12 MHz ultrasound probe (LOGIC S6, GE) in carotid setting. Results: IMT of common carotid artery (56.8 ΁ 7.6 in cases versus 49.8 ΁ 7.3 in controls), internal carotid artery (56.9 ΁ 6.03 in cases versus 49.6 ΁ 6.9 in controls), and both common and internal carotid artery (56.6 ΁ 6.7 in cases versus 49.7 ΁ 6.9 in controls) were significantly higher in PCOS patients than healthy women (P < 0.001). Conclusions: In summary, results demonstrated that carotid artery thickness as a risk for premature atherosclerosis in patients with PCOS is higher than healthy subjects. And hence care and monitoring of PCOS women with these risk factors sounds to be important and necessary.