Deep-brain stimulation (DBS) surgery involves placing electrodes within specific deep-brain target nuclei. Surgeons employ MR imaging for preoperative selection of targets and computed tomography (CT) imaging for designing stereotactic frames used for intraoperative placement of electrodes at the targets. MR distortion may contribute to target-selection error in the MR scan and also to MR-CT registration error, each of which contributes to error in electrode placement. In this paper, we analyze the error contributed by the MR distortion to the total DBS targeting error. Distortion in conventional MR scans, both T1 and T2 weighted, were analyzed for six bilateral DBS patients in the typical areas of brain using typical scans on a 3-T clinical scanner. Mean targeting error due to MR distortion in T2 was found to be 0.07 ± 0.025 mm with a maximum of 0.13 mm over 12 targets; error in the T1 images was smaller by 4%.