Our aim was to investigate wall thickening (WT) pattern of atherosclerotic basilar artery stenosis with three-dimensional volumetric isotropic turbo spin echo acquisition (3D VISTA), and the relationship with clinical characteristics. Twenty consecutive patients with atherosclerotic basilar artery stenosis were prospectively enrolled. All cross-sectional slices on VISTA images of basilar arteries were assessed, and classified as eccentric or concentric WT. Clinical characteristics and degree of stenosis were compared between the patients with different wall WT pattern. Wall abnormalities were identified in 568 cross-sectional slices in basilar arteries of 20 patients including eccentric WT in 497 (87.5 %) slices, and concentric WT in 71 (12.5 %) slices. In 11 of 20 patients, all the cross-sectional slices (293 slices) showed eccentric WT. In 9 of 20 patients, the cross-sectional slices (275 slices) showed both eccentric WT (204 slices, 74.2 %) and concentric WT(71 slices, 25.8 %). No lesion showed only concentric WT. At the slices of maximum luminal narrowing sites, only one patient showed concentric WT. Symptomatic stenosis was more common in the patients with mixed WT (eccentric and concentric), compared to patients with only eccentric WT (100 vs 54.5 %, p = 0.038). Atherosclerotic basilar artery stenosis could show both eccentric and concentric WT based on each slice analysis. Concentric WT was found in near half of the patients, but tended to locate in minimal slices. No lesion was entirely concentric. Lesions with mixed WT (concentric and eccentric) might represent advanced atherosclerosis with high risk of ischemic event.