The relationships among diabetes mellitus (DM), brainstem infarctions (BSIs) and involvement of the basilar artery (BA) were investigated in 254 patients with acute cerebral infarctions detected on magnetic resonance (MR) imaging. Radiological findings included lesion topography and size (mm2) of BSIs on MR images, and the extent of BA stenosis measured by MR angiography. Adjusted logistic regression analyses showed that DM (OR 4.018; p = 0.0006) and BA stenosis (OR 1.003 per 1 mm; p < 0.0001) had an independent association with the incidence of BSIs, but the lesion size of the BSIs was only associated with BA stenosis (β coefficient 0.280; p < 0.0001). Diabetic patients showed significantly more frequent isolated pontine infarctions and a lesser degree of BA stenosis (p < 0.005) compared to non-diabetic patients. Preferential involvement of the pons and smaller vessels may be characteristics of diabetic patients.