The purpose of this study is to evaluate the correlation between variation of the vertebral artery (VA) and the incidence of pontine infarction. A total of 206 patients were examined using magnetic resonance imaging (MRI) and 3-dimension time-of-flight MR angiography (MRA) of the brain. Of these, 54 patients had pontine infarctions (23 symptomatic and 31 asymptomatic), and the majority of them were located in the pontine base. The sites of dominant lesion in the pons were right in 18 cases, left in 8 cases, and bilateral in 28 cases. The number of patients with VA asymmetry (the ratio of internal diameters 1:2 or more) were 89 (43.2%). Of these, 67 patients had small diametric VA of right side, and 22 of left side. Among the 117 patients with normal VA pattern, 19 (16.2%) had infarction, while among the 89 patients with VA asymmetry, 35 (39.3%) had infarction. The patients with small diametric VA of right side significantly had infarctions in the same side of the pons. The results of this study suggest that VA asymmetry is considered to be one of the risk factors of pontine infarction and that MRA can be useful in the examination of the cerebral artery as a valuable and non-invasive screening method.