Abstract: Back ground and objectives: Polycystic ovary syndrome is a common disorder with endocrine and reproductive abnormality which lead to high risk for development of premature atherosclerotic heart disease in reproductive age group. There are many risk factors in women with polycystic ovary syndrome that associated with risk of atherosclerosis. This study was undertaken to evaluate the level of homocysteine as a novel cardiovascular risk marker in polycystic ovarian syndrome women compared to healthy controls.