To evaluate the efficacy of magnetic resonance imaging in brainstem stroke, we studied 21 cases of clinically definite brainstem ischemic stroke with brain magnetic resonance imaging (MRI) and conventional computed tomography (CT). MRI demonstrated brainstem lesions in 79% of the cases (16.5 out of 21), while CT revealed 33% (7 out of 21) when cases with suspicious lesions counted as 0.5. Although MRI was done a few days later than CT in most cases, MRI was superior to CT in detecting the number and the size of ischemic lesions, with clear delineation of anatomy and visualization of the status of the blood flow in the vertebral-basilar artery. Disappearance of the flow signal void in the basilar artery can be an important clue in diagnosing occlusion or thrombus of the basilar artery. By delineating the extent and the location of the infarction, MRI findings allowed an interpretation of whether the ischemic vessel is a small basilar branch or a large vessel vertebral or basilar artery.