Computer-navigated pedicle screw insertion is applied to the thoracic and lumbar spine to attain high insertion accuracy and a low rate of screw-related complications. However, some in vivo and in vitro studies have shown that no advantages are gained with the use of navigation techniques compared to conventional techniques. Additionally, inconsistent conclusions have been drawn in various studies due to different population characteristics and methods used to assess the accuracy of screw placement. Moreover, it is not clear whether pedicle screw insertion with navigation techniques decreases the incidence of screw-related complications. Therefore, this study was sought to perform a meta-analysis of all available prospective evidence regarding pedicle screw insertion with or without navigation techniques in human thoracic and lumbar spine. We considered in vivo comparative studies that assessed the results of pedicle screw placement with or without navigation techniques. PubMed, Ovid MEDLINE and EMBASE databases were searched. Three published randomized controlled trials (RCTs) and nine retrospective comparative studies met the inclusion criteria. These studies included a total of 732 patients in whom 4,953 screws were inserted. In conclusion, accuracy of the position of grade I, II, III and IV screws and complication rate related to pedicle screw placement were significantly increased when navigation techniques were used in comparison to conventional techniques. Future research in this area should include RCTs with well-planned methodology to limit bias and report on validated, patient-based outcome measures.