Deep brain stimulation (DBS) has been established as an invasive therapy of treatment of severe forms of movement disorders such as Parkinson’s disease (PD). Most patients with PD are treated by DBS in the area of the subthalamic nucleus (STN). However, the exact location of the optimal target site and the targeting procedures are is still under debate.In a consecutive PD patient series (2010–2011) we compared preoperative MRI planning, intraoperative target adjustment and postoperative CT target reconstruction. The localizations of the DBS electrodes were documented in the mean 3-dimensional Morel-Atlas of the basal ganglia and the thalamus.The series includes 20 patients (8 female, 12 male, median age 62years; 40 implantations). The optimal stimulation site had median coordinates Xlat=±12mm, Yap=−1.8mm, Zvert=−2.8mmOf the implanted electrodes, 94% are in contact with the STN of the atlas. Median penetration into STN was 6mm.There was a significant difference between the initially planned site and the coordinates of the optimal stimulation site (median 2.2mm). The stimulation site was – on average – more anterior and more dorsal.The optimal stimulation site was within STN in 75% and within 2mm of STN in 100% of penetrations.The deviation between preoperative planning and postoperative CT reconstruction demonstrate the importance of intraoperative recording of neuronal activity and clinical testing of stimulation efficiency.The variability between the individual anatomical STN-configurations is sufficiently small to permit the application of the averaged atlas.Among all anatomical structures, stimulation sites within the STN proper were most efficient in improving clinical outcome.