Abstract: Objective To evaluate the association between plasma homocystein (Hcy) level and cryptogenic ischemic stroke(CIS), and analyze its clinical significance. Methods Patients with CIS and normal controls were consecutively recruited in the ward neurological department and outpatient department of Beijing Shijingshan Hospital to measure their plasma Hcy level by fluorescence polarization immunoassay and the severity of atherosclerotic plaques in carotid arteries and aortic arches were evaluated by ultrasonography. Results Thirty-two CIS patients and 47 normal controls were collected in total. The plasma Hcy level of CIS patients was significantly higher than that of normal controls 21.83 vs 15.73, P=0.005. Whereas, Hcy level failed to demonstrate an independent association with CIS after adjustment of confounding risk factors in multivariate logistic regression. Then all subjects were stratified by the presence of aortic or carotid plaques respectively. Then, plasma Hcy level was found to be an independent risk factor for CIS patients with aortic plaques (OR=1.55, 95%CI: 1.53-1.57, P=0.023) after adjusting confounding risk factors.Conclusion Hcy level shows association with CIS although Hcy level does not seem to be an independent risk factor for CIS; it is valuable to measure and control plasma Hcy level particularly in CIS patients with aortic plaques.