Objective This study was to investigate the relationship between the variation of vertebrobasilar artery system and the etiology of transient ischemic attack. Methods Fifty patients with transient ischemic attack from January 2005 to December 2014 were enrolled in this study. Fifty healthy subjects were enrolled in the observation group and the control group Group, all underwent CT angiography to assess vertebrobasilar artery variation. Results In the observation group,17 cases of vertebrobasilar arterial variability were found in 50 cases, including 6 vertebral artery tortuosity, 4 congenital small side development, 2 small congenital bilateral small side development , vertebral artery window 2，basilar artery window 1.2 abnormal origin of basilar arteries. Two of the 50 patients in the control group had 2 basilar arteries. Exposure rates were statistically different between the two groups (χ2 =27.77, P<0.001). Abnormal basilar artery system was an independent risk factor for transient ischemic attack (OR=20). Conclusion There is a high correlation between the variation of basilar artery system and the etiology of transient ischemic attack. CTA can provide a diagnosis and prediction of transient ischemic attack by showing the anatomic relationship of vertebrobasilar artery.