Background The location of plaque may be associated with the vascular geometry. Aim We aimed to examine the relationship between the geometry of middle cerebral artery and the plaque location detected by high-resolution magnetic resonance imaging. Methods Among patients with a single subcortical infarction without a significant middle cerebral artery stenosis on magnetic resonance angiography, those with a plaque detected from high-resolution magnetic resonance imaging were prospectively enrolled. The shape of middle cerebral artery was measured from the coronal view, and was classified as straight, U-shaped, inverted U-shaped, and S-shaped. The location of the plaque was divided into superior and inferior, and analyzed according to the shape of middle cerebral artery. Results Among the 40 patients, the shape of middle cerebral artery was straight in 7 (17·5%), U-shaped in 10 (15·0%), inverted U-shaped in 11 (27·5%), and S-shaped in 12 patients (30·0%). The superior plaque was more closely associated with straight (85·7%) or U-shaped middle cerebral arteries (90·0%), whereas inverted U-shaped (81·8%) and S-shaped middle cerebral arteries (75·0%) were more often associated with inferior plaque. The prevalence of symptomatic plaque was higher in superior than inferior plaques (70·0% vs. 25·0%, P = 0·004). Multivariate analysis showed that straight and U-shaped middle cerebral artery was the only significant factor associated with the superior plaque. Conclusion The shape of middle cerebral artery may be a factor determining the location of early atherosclerotic plaque.