Surgery of intrinsic brainstem lesions is extremely dangerous, consequently the knowledge of anatomy and safe entry zones is extremely important. The technological progress was achieved with the widespread clinical use of intraoperative neurophysiological monitoring (IONM) which has proven to further improve the safety of operating on intrinsic brainstem lesions. The relevance of the study is conditioned by the fact that the tumor alters the normal anatomy and distorts the location of well-known landmarks and structures. In this regard, this paper is directed at identification of the placement of conductive pathways in the thickness of the brain stem and directly in the depth of the lesion (in the tumor or cavern), respectively to the surgical manipulations aimed at injury prevention. The results were achieved by a retrospective review of medical reports. The paper represents the results of surgical treatment of 42 patients with brainstem lesions, reviews the localization of the lesion and neurological status of patients, describes available methods of intraoperative monitoring (IOM) and on-line techniques for the brainstem surgery. The materials of the paper are of practical significance for the development of brainstem surgery with IONM modifications for wider and more comfortable use by neurosurgeons.