To develop an objective method for detecting multiple sclerosis (MS) brainstem lesions, magnetic resonance (MR) images (multiple planar, spin-echo, acquired in three planes of section) of sixteen MS patients and fourteen normal subjects were analyzed with an algorithm that detected regions with a relatively increased intensity on both a spin-echo image and a T2 image. To be considered a lesion, such regions had to overlap in at least two orthogonal planes. Using a digitized atlas of the human brainstem, the lesion locations were mapped with respect to the brainstem anatomy. This method was evaluated by comparing the location of MS lesions with the brainstem auditory evoked potentials obtained from these subjects. Brainstem lesions were detected in five MS patients; four had lesions impinging upon the auditory system and one did not. All four had abnormal evoked potentials. The fourteen normal subjects, the one MS patient with brainstem lesions outside the auditory pathway, and the eleven other MS patients with no brainstem lesions all had normal evoked potentials. The requirement that lesions be detected in at least two planes of section greatly improved the specificity of the algorithm. The consistency between the MR and brainstem auditory evoked potentials results supports the validity of this imaging analysis algorithm for objectively localizing brainstem lesions.