The deep brain stimulation (DBS) is an effective treatment modality of the functional neurosurgery for disorders such as Parkinson's disease, essential tremor and generalized dystonia. Recently, the targets of DBS for treatment of Parkinson's disease are the thalamus, the Globus pallidus and subthalamic nucleus (STN). The STN-DBS induces improvements in axial motor fluctuation and the on-off phenomenon. The important problem for STN-DBS is that DBS is inserted properly into the STN for good results. The STN is a small body in the deep brain structures. We cannot understand the STN clearly because of its small size and complex shape. The topographical information of deep brain structures has been essential for accurate stereotactic placement of the stimulating electrode of DBS. The target of a deep brain structure is based on the Schaltenbrand and Wahren atlas (S-W atlas). The S-W atlas consists of two-dimensional images such as a coronal section. For this reason, it is difficult to understand localization and the shape of deep brain structures spatially, especially of the subthalamic nucleus on S-W atlas. The three-dimensional image is a useful tool for diagnosis and preoperative planning, because it can easily give neurosurgeons the vivid spatial image of complex structures. We studied a practical use of a three-dimensional atlas of deep brain structures in functional neurosurgery. We devised a three-dimensional atlas to see an image at a free angle on a personal computer. It provided us with more useful information about structures than ones by two-dimentional images. Three-dimensional atlas also helped us make a decision for placement of the deep brain electrode and appropriate electrophysiological recording.