The method of three-dimensional reconstruction of structures and lesions in the brainstem was developed by using a personal computer to visualize the affected sites in some cranial nuclei and long tracts. Outlines of brainstem structures and lesions were digitalized manually by tracing the atlas of the human brainstem and CT or MR images. Four outlines of the brainstem, the medulla, lower pons, upper pons and midbrain, and the outlines of any parenchymal structures were taken at every point 2 mm in thickness. These were used as the standard visualization of the atlas. The CT and MRI, which show outlines of the lesions, were taken on the vertical planes to the floor of the fourth ventricle, one of which included the fastigium, at every point 3 to 5 mm in thickness. These two kinds of outlines, taken from the atlas and the CT/MRI, were reconstructed three-dimensionally with commercial 3-D software. It took only 20 to 25 minutes for the digitalization and the 3-D reconstruction. Three-dimensional display of small structures, which were difficult to identify on CT or MRI, and lesions would enable the visualization of their anatomical relations and make possible the detection of the affected sites, not only in the axial but in the longitudinal direction. Correspondence between the affected sites on 3-D and the neurophysiological examinations (ABR, SSEP) confirms that our 3-D method is adequate for use in the anatomical diagnosis of affected sites in any small structure in the brainstem.