Purpose <p>Accurate placement of electrodes within the subthalamic nucleus is critical for deep brain stimulation (STN-DBS) in Parkinson’s disease (PD). Our objective was to compare microelectrode recording (MER) and an automatic MR-based segmentation tool (BrainLab Elements^TM) for STN targeting and the determination of STN boundaries.</p> Methods <p>Seventy-eight PD patients were included. Electrode placement within the STN and STN entry and exit points were determined by both methods and compared for concordance.</p> Results <p>Of 344 trajectories, 269 were inside the STN, with good concordance of both techniques (Fleiss’ kappa 0.721, [95%CI 0.623, 0.819]). Concordance of MER and MR-based for the selection of the optimal trajectory was good (Fleiss’ kappa 0.693, [95%CI 0.578, 0.808]), with less than 2.75mm difference between MER and MR-based for the STN entry (upper limit of agreement 2.752 [95%CI 2.365 to 3.138] mm; lower limit of agreement -2.406 [95%CI -2.793 to -2.020] mm) and exit points (upper limit of agreement 2.750 [95%CI 2.351 to 3.149] mm; lower limit of agreement -2.577mm [95%CI -2.976 to -2.178]).</p> Conclusion <p>We demonstrated that MER and MR-based segmentation have a good concordance to determine STN boundaries during DBS surgery.</p>