Background: Studies of deep brain stimulation (DBS) require accurate electrode localization and image registration. We used anatomical fiducials to investigate localization and registration errors in patients who underwent subthalamic nucleus (STN) DBS for Parkinson’s disease (PD). Methods: We conducted a retrospective analysis of patients who underwent bilateral STN DBS for PD. Pre and post operative MRI scans were non-linearly normalized to a standard template (MNI152NLin2009bAsym). Four raters localized DBS electrodes (Lead-DBS), the anterior commissure (AC) and posterior commissure (PC). Errors between rater localizations were calculated (fiducial localization error; FLE). We transformed AC and PC coordinates from template to patient space to calculate the fiducial registration error (FRE)Results: Ninety-nine patients were analyzed, with a median FLE of 0.76mm, 0.74mm, 0.71mm and 0.66mm for the right electrode, left electrode, AC and PC respectively (no significant difference, Wilcoxon sign rank). The median FRE was 1.59mm for AC and 1.21mm for PC, significantly higher than FLE at those coordinates (Wilcoxon sign rank, p<0.001). Conclusions: Raters can accurately localize DBS electrodes, AC and PC from clinical images with sub-millimetric accuracy. Higher FREs at AC and PC suggested registration errors may contribute more than localization errors to electrode uncertainty in a common space.