BACKGROUNDC2 pedicle screw placement in patients with basilar invagination (BI) is fraught with risks because of a high incidence of anatomical variations and high-riding vertebral artery (HRVA). However, no study can be found in the literature that attempted to identify the ideal entry point and trajectory through the C2 pedicle in BI patients with HRVA. PURPOSETo investigate the parameters of ideal entry point and trajectory for C2 pedicle screw placement in BI patients with HRVA and compare them with those in BI patients without HRVA and patients without BI as control. These parameters would serve as a guide to pedicle screw placement. STUDY DESIGNA retrospective comparative study. PATIENT SAMPLEA total of 396 patients (198 consecutive BI patients and 198 matched patients without BI as control) and 792 unilateral pedicles from April 2017 to October 2021 at two medical centers were included. OUTCOME MEASURESThe insertion parameters of mediolateral angle, surface distance, cephalad angle, and vertical distance from the superior border of the lamina were the primary outcome measures for the reference of C2 pedicle screw placement. Furthermore, factors that affect the primary insertion parameters were assessed via multiple linear regression analyses. METHODAccording to the diagnosis of BI and HRVA, the unilateral pedicles were assigned into HRVA of BI, non-HRVA of BI, HRVA of control, and non-HRVA of control groups. Subgroup analyses based on Goel types A and B were also performed. Moreover, vertebral artery (VA) anomalies that might result in potentially serious complications were identified and systematically compared. RESULTSThe measurements of insertion parameters in BI patients with HRVA indicated a mean mediolateral angle of 27.42°, a mean cephalad angle of 43.02°, a mean surface distance of 9.74 mm, and a mean vertical distance from the superior border of the lamina of 3.85 mm. Compared with that in BI patients without HRVA, the measurements suggested that the entry point in BI patients with HRVA should be shifted upward by 0.38 mm and the trajectory should be angled cephalad by 6.05° and medially by 4.78°. In the control group, changes in the insertion parameters between HRVA and non-HRVA showed a similar trend to the BI group. Multiple linear regression showed that mediolateral angle was significantly associated with the male gender (B=−0.930, p=.017) and the diagnoses of HRVA (B=6.964, p<.001), Goel type A (B=−1.656, p=.003), and Goel type B (B=0.981, p=.030). Moreover, cephalad angle was significantly associated with the length of lateral mass (B=−0.319, p=.001) and the diagnoses of HRVA (B=3.254, p<.001) and Goel type A (B=6.924, p<.001). The VA anomalies were significantly higher in the BI group than in the control group. CONCLUSIONSThe insertion parameters of the ideal entry point and trajectory for C2 screw placement in BI patients with HRVA were remarkably different from those of non-HRVA of BI, HRVA of control, and non-HRVA of control cohorts. Preoperative 3D computed tomography (CT) and CT angiography are highly recommended in such patients to improve intraoperative safety and reduce postoperative complications.