Subthalamic nucleus is one of the most interesting structures of basal ganglia. Neurosurgical stimulation of STN has improved condition of many patients with levodopa resistant Parkinson’s disease. However, it also led to many unwanted side-effects due to the inconclusive delineation of STN segments’ borders. Previous studies which dealt with this topic did not produce definite answer about number and location of STN segments. In this study we analyzed the distribution of five neuronal markers in the STN: NeuN, calretinin, calbindin, parvalbumin and nNOS. All markers were positive in STN except calbindin. The largest population of neurons in STN is positive for nNOS, and the smallest population is calretinin positive. By analyzing the spatial distribution of neurons in STN we could not determine the borders between segments nor any individual segments in STN. Furthermore, we analyzed 1,5 and 3T MR images to determine STN segments. We were not able to determine any segments on these images. However, we analyzed the precision of DBS electrode location in the STN and based on these data we created “virtual” motor segment of STN. The stimulation within these “virtual segment” provided satisfactory clinical results in controlling symptoms of Parkinson’s disease.