Hybrid-operating rooms (hybrid-OR) combine high-resolution 2D images and 3D-scans with the possibility of 3D-navigation and allow minimal invasive pedicle screw placement even in the upper thoracic spine. The disadvantage of high cost and increased radiation needs to be compensated with high accuracy and safety. The hybrid operating room consists of a floor-based flat-panel robotic C-arm with 3D-scan capability (Artis Zeego, Siemens; Germany) combined with navigation (BrainLAB Curve, BrainLAB; Germany). Through a minimally invasive incision, a Jamshidi needle was advanced through the pedicle and a K-wire was placed. If 2D image quality did not allow safe placement 3D-navigation was used to place the K-wire. Position was controlled through a 3D-Scan and corrected if necessary before screw placement. Postoperative CTs evaluated screw perforation grade with grade I when completely within the pedicle, II < 2 mm, III 2–4 mm, and IV > 4 mm outside the pedicle. Overall, 354 screws were placed in T1–T6, 746 in the lower thoracic spine T7–T12 and 645 in the L1-L5. Navigation was mainly used in upper thoracic spine cases (31 of 57). In 63 out of 326 cases K-wire was corrected after the 3D-Scan. Overall, 99.1% of the screws showed perforation less than 2 mm. Mean radiation was 13.3 ± 11.7 mSv and significantly higher in the upper thoracic spine and in navigated procedures. Despite higher costs and radiation, the hybrid-OR allows highest accuracy and therefore patient safety in minimal invasive pedicle screw placement in the thoracic and lumbar spine.