The association of atherosclerosis (AS) and Human cytomegalovirus (HCMV) infection was studied. AS plays an important role in the brain stroke and HCMV infection is supposed to be involved in the process of atherosclerotic formation. The presence of HCMV DNA and antigens was examined in the internal carotid arteries collected from 35 patients with ischemic stroke and from 20 patients from the control population. All patients belonged to the ethnic Han population in China. Three methods, immunohistochemistry (IHC), hybridization in situ (HIS), and PCR were used to detect the HCMV immediate early (IE) and late (L) antigens as well as viral DNA in vessel walls. Levels of HCMV IE gene/protein were significantly higher in the stroke group than in control group detected by the three methods (IHC 34.3% vs. 10.0%; HIS 40.0% vs. 10.0; PCR 60.0% vs. 30.0%). However, there was no significant difference in the levels of HCMV L gene/protein between these two groups of patients (IHC 11.4% vs. 5.0%; HIS 11.4% vs. 10.0%; PCR 20.0% vs. 20.0%). We concluded that the presence of HCMV IE antigen and HCMV DNA in the vessel wall was associated with the pathological process of AS formation.