This study was designed to report our preliminary experience with stabilization procedures for complex craniovertebral junction malformation (CVJM) using intraoperative computed tomography (iCT) with an integrated neuronavigation system (NNS). To evaluate the workflow, feasibility and clinical outcome of stabilization procedures using iCT image-guided navigation for complex CVJM. The stabilization procedures in CVJM are complex because of the area's intricate geometry and bony structures, its critical relationship to neurovascular structures and the intricate biomechanical issues involved. A sliding gantry 40-slice computed tomography scanner was installed in a preexisting operating room. The images were transferred directly from the scanner to the NNS using an automated registration system. On the basis of the analysis of intraoperative computed tomographic images, 23 cases (11 males, 12 females) with complicated CVJM underwent navigated stabilization procedures to allow more control over screw placement. The age of these patients were 19-52 years (mean: 33.5 y). We performed C1-C2 transarticular screw fixation in 6 patients to produce atlantoaxial arthrodesis with better reliability. Because of a high-riding transverse foramen on at least 1 side of the C2 vertebra and an anomalous vertebral artery position, 7 patients underwent C1 lateral mass and C2 pedicle screw fixation. Ten additional patients were treated with individualized occipitocervical fixation surgery from the hypoplasia of C1 or constraints due to C2 bone structure. In total, 108 screws were inserted into 23 patients using navigational assistance. The screws comprised 20 C1 lateral mass screws, 26 C2, 14 C3, or 4 C4 pedicle screws, 32 occipital screws, and 12 C1-C2 transarticular screws. There were no vascular or neural complications except for pedicle perforations that were detected in 2 (1.9%) patients and were corrected intraoperatively without any persistent nerves or vessel damage. The overall accuracy of the image guidance system was 98.1%. The duration of interruption during the surgical process for the iCT was 8±1.5 minutes. All patients were clinically evaluated using Nurick grade criteria and for neurological deficits 3 months after surgery. Twenty-one patients (91.3%) improved by at least 1 Nurick grade, whereas the grade remained unchanged in 2 (8.7%) patients. Craniovertebral stability and solid bone fusion was achieved in all patients. NNS was found to correlate well with the intraoperative findings, and the recalibration was uneventful in all cases and had an accuracy of 1.8 mm (range, 0.6-2.2 mm). iCT scanning with integrated NNS was found to be both feasible and beneficial in the stabilization procedures for complex CVJM. In this unusual patient population, the technique seemed to be of value for negotiating complex anatomy and for achieving more control over screw placement.