Neuronavigation is a kind of image-guided surgery used during neurosurgical procedures. Based on specific equipment which is compatible with the software calculating and processing the patient’s data; this method allows the determination of the location of anatomical structures and visualisation of surgical instruments in the operative field. Although standard brain dissection is still the best method of neuroanatomical training, some limitations occur. The most important of these is the inability of conversion from three-dimensional (3D) view to flat pictures of the brain structures, as viewed on computed tomography (CT) and magnetic resonance imaging (MRI), being essential in neuroanatomical training nowadays. The aim of the study was the implementation of a neuronavigating system for brain anatomy training purposes. The study was performed on 10 human brain hemispheres, dissected due to classical methods (standard brain anatomical sections, stepwise ventricular system opening and partial dissection of white matter tracts using Klingler’s dissection technique). The material was scanned in a 1.5 T magnetic resonance scanner using a modified neuronavigation protocol. The brains were prepared before dissection as proposed by Klingler. The subsequent steps of the dissection were documented with a digital camera. The progress of the dissection was visualised using the neuronavigation system (Medtronic Stealth Station Treon) with cranial application software. In the course of the study, numerous 3D and 2D images were obtained. The images were related to each other and linked anatomical structures in the specimen with their appearance on CT and MRI scans. The implementation of a neuronavigation system for brain structures dissection facilitates visualization and understanding of their proper location. This new method offers a constant and precise orientation and simplifies understanding of the relation of the 3D view of a specimen to that of the 2D image.