Aims: Various studies could show that computer assisted pedicle screw insertion can reduce pedicle perforation rate. We conducted this study to verify if pedicle screw navigation can also avoid neurological complications. Methods: Within 20 months 112 patients were stabilised with 584 pedicle screws in the thoracolumbar spine (Th1-L5). 333 screws were inserted using a CT-based navigation system, 251 srews with conventional technique. Postoperatively, screw positons were assessed by an independent radiologist using CT-scans. Neurological complications and revision surgery were noted. Results: 47 (14.1%) of navigated screws perforated pedicle wall, 13 (28%) to medial side with 2 screws more than 4 mm. One screw (0.3%) had to be changed due to medial perforation of 6 mm in Th4. In the conventional group 60 (29.9%) screws perforated pedicle wall, 13 (22%) to medial side with 3 screws more than 4 mm. One patient had to be reoperated due to radicular deficit caused by a medial perforated screw in L1 (0.4%)Conclusion: CT-based navigation of pedicle screws decreased pedicle perforation rate significantly. However, considerable medial perforations up to 6 mm could not be avoided entirely. The rate of neurologic complicatons and revision surgery was the same in both computer assisted and conventional group.