Objective: To answer the question of whether the anatomical center of the subthalamic nucleus (STN), as calculated indirectly from stereotactic atlases or by direct visualization on magnetic resonance imaging (MRI), corresponds to the best functional target. Since the neighboring red nucleus (RN) is well visualized on MRI, we studied the relationships of the final target to its different borders. Methods: We analyzed the data of 23 PD patients (46 targets) who underwent bilateral frame-based STN deep brain stimulation (DBS) procedure with microelectrode recording guidance. We calculated coordinates of the active contact on DBS electrode on postoperative MRI, which we referred to as the final “functional/optimal” target. The coordinates calculated by the atlas-based “indirect” and “direct” methods, as well as the coordinates of the different RN borders were compared to these final coordinates. Results: The mean ± SD of the final target coordinates was 11.7 ± 1.5 mm lateral (X), 2.4 ± 1.5 mm posterior (Y), and 6.1 ± 1.7 mm inferior to the mid-commissural point (Z). No significant differences were found between the “indirect” X, Z coordinates and those of the final targets. The “indirect” Y coordinate was significantly posterior to Y of the final target, with mean difference of 0.6 mm (p = 0.014). No significant differences were found between the “direct” X, Y, and Z coordinates and those of the final targets. Conclusions: The functional STN target is located in direct proximity to its anatomical center. During preoperative targeting, we recommend using the “direct” method, and taking into consideration the relationships of the final target to the mid-commissural point (MCP) and the different RN borders.