Introduction: Intraoperative microelectrodes recording with the Ben Gun microdrive system are often used during DBS surgery. An accurate location of these microelectrodes will directly influence the interest of this recording. We have studied the imprecision of implantation of these microelectrodes. Methods: We have analyzed the stereotactic position of 135 microelectrodes implanted with the Ben Gun microdrive during DBS surgery of 16 patients with advanced Parkinson’s disease. An intracranial CT was obtained and integrated to a stereotactic planification system. We recorded the stereotactic coordinates of the 5 microelectrodes inserted simultaneously in a cross-shape. The coordinates of each microelectrode were compared with coordinates of the other 4 electrodes inserted simultaneously with the Ben Gun and visible on the same iCT image. Thus, this procedure avoids errors from image fusion and from brain shift. We calculate (1) the three-dimensional Euclidian deviation of microelectrodes, (2) the deviation in X- and Y-axes on reconstructed probe’s eye view MR images, and (3) the deviation from the 2-mm theoretical distance between the central electrode and 4 satellite microelectrodes. Results: The median deviation was 0.64 mm in 3-D and 0.58 mm in 2-D probe’s eye view. Satellite electrodes were located from the central electrode theoretically at 2.0 mm and practically within the range 1.9–2.1 mm, 1.5–2.5 mm, 1.0–3.0 mm, and 0.5–3.5 mm for, respectively, 9.3%, 53.7%, 88.0%, and 98.1%, thus highlighting the significant deviation from the theoretical distance. Position imprecisions were similar for the 4 satellite microelectrodes. The imprecision was similar in X-axis and Y-axes and statistically less in Z-axis. For bilateral implantation, the second implantation of the same patient was not associated with a greater risk of deviation of the microelectrodes than for the first side implanted. Conclusion: A significant percentage of microelectrodes for MER can deviate substantially from their theoretical target during DBS procedures. An iCT can be used to estimate the potential deviation of microelectrodes and improve the interpretation of MER during the procedure.