Objective: During deep brain stimulation (DBS) surgery, microelectrode recording (MER) leads to target refinement from the initial plan in 30% to 47% of hemispheres; however, it is unclear whether the DBS lead ultimately resides within the MER-optimized target in relation to initial radiographic target coordinates in these hemispheres. This study aimed to determine the frequency of discordance between radiographic and neurophysiologic nucleus and whether target optimization with MER leads to a significant change in DBS lead location away from initial target. Methods: Consecutive cases of DBS surgery with MER using intraoperative computed tomography were included. Coordinates of initial anatomic target (AT), MER-optimized target (MER-O) and DBS lead were obtained. Hemispheres were categorized as “discordant” (D) if there was a suboptimal neurophysiologic signal despite accurate targeting of AT. Hemispheres where the first MER pass was satisfactory were deemed “concordant” (C). Coordinates and radial distances between 1) AT/MER-O; 2) MER-O/DBS; and 3) AT/DBS were calculated and compared. Results: Of the 273 hemispheres analyzed, 143 (52%) were D, and 130 (48%) were C. In C hemispheres, DBS lead placement error (mean ± standard error of the mean) was 0.88 ± 0.07 mm. In D hemispheres, MER resulted in significant migration of DBS lead (mean AT-DBS error 2.11 ± 0.07 mm), and this distance was significantly greater than the distance between MER-O and DBS (2.11 vs. 1.09 mm, P < 0.05). Directional assessment revealed that the DBS lead migrated in the intended direction as determined by MER-O in D hemispheres, except when the intended direction was anterolateral. Conclusions: Discordance between radiographic and neurophysiologic target was seen in 52% of hemispheres, and MER resulted in appropriate deviation of the DBS lead toward the appropriate target. The actual value of the deviation, when compared with DBS lead placement error in C hemispheres, was, on average, small.