This report is in two parts. First, a case report on a 20-year-old man with a localized brain stem contusion. Second, in order to elucidate the mechanism of this injury, an anatomical study was performed. Ten cadaver heads were analysed to reveal the variations of spatial anatomy around the tentorial incisura. The lateral tentorial incisura (lateral to brain stem) was situated at the level of pontomesencephalic junction and nearest to the brain stem along its course. The shortest distance between them averaged 1.0 mm (0-4 mm). Based on these findings, primary brain stem injury caused by tentorial incisura occurs at its lateral portion due to the shortest distance to the brain stem and near the level of pontomesencephalic junction. In patients with a tentorial incisura closely related to or touching the brain stem, tentorial coup injury to the brain stem may occur even with a relatively minor injury. In our case, repeated CT and MRI proved that the location of contusion was at the pontomesencephalic junction, coinciding with the level of the tentorial edge. The injury started at the surface of brain stem. The tentorial edge was close to brain stem in this case. These radiological findings support the hypothesis that the brain stem contusion was caused by a tentorial coup injury.