To assess screw malposition rates and complications associated with pedicle screw insertion using 3D navigation technology. A retrospective study was undertaken for all cases where O-arm® and StealthStation® systems were used over a 2-year period. The primary outcome measure was return to theatre rates for pedicle screw malposition. A total of 938 screws were inserted (934 thoracolumbar and 4 cervical), and 103 patients underwent spinal fixation using O-arm® and StealthStation® navigation. 64 were revision cases and 39 primary cases. Average number of levels was 4.6. There were a total of 10 complications: 3 infections, 1 DVT, 1 PE, 1 fast atrial fibrillation (AF), 1 screw malposition, 1 non-union, 1 undisplaced vertebral body fracture and 1 nerve root compression following osteotomy. The percentage return to theatre for screw malposition using 3D navigation was 1% of patients and 0.1% of pedicle screws. No patients developed permanent neurological compromise. These systems provide accuracy that is comparable to traditional 2D fluoroscopic techniques. We advocate their use in the safe insertion of pedicle screws in complex revision deformity cases where original anatomical landmarks are absent or obscured. We also believe that radiation exposure is considerably less with navigation especially in these complex and revision cases.