Previous studies have demonstrated that Helicobacter pylori infection is associated with coronary atherosclerotic heart disease, but the correlation between Helicobacter pylori infection and ischemic stroke remains unclear. The present study assessed the effects of Helicobacter pylori infection on atherothrombotic stroke. This study included 115 individuals with atherothrombotic stroke, all of whom were patients receiving treatment at the Department of Neurology, Aerospace Central Hospital (Aerospace Clinical Medical College Affiliated to Peking University) in China, from March 2006 to July 2009. In addition, 131 controls without the history of cardiovascular disease, cerebrovascular disease or atherothrombosis were also enrolled in the study. Results show that the Helicobacter pylori-IgG positive rate was greater in the atherothrombotic stroke patients than in the controls, but the difference was not statistically significant (67.8% vs. 61.8%, OR = 1.301, 95%CI: 0.769-2.203, P = 0.327). After correction for potential risk factors for Helicobacter pylori infection and known risk factors for ischemic stroke, no significant difference was detected between them (OR = 1.278, 95%CI: 0.667-2.449, P = 0.459). These results indicate that there is no specific correlation between Helicobacter pylori infection and atherothrombotic stroke. This finding requires further verification in large-sample prospective studies.