High-riding vertebral artery (HRVA) and narrow C2 pedicles (C2P) pose a great risk of injuring the vessel during C2 pedicle or transarticular screw placement. Recent meta-analysis revealed a paucity of European studies regarding measurements and prevalence of these anatomical variants. Three hundred eighty-three consecutive cervical spine CT scans with 766 potential screw insertion sites were analyzed independently by two trained observers. C2 internal height (C2InH), C2 isthmus height (C2IsH), and C2P width were measured. Kappa statistics for inter- and intraobserver reliability as well as for inter-software agreement were calculated. HRVA was defined as C2IsH of ≤ 5 mm and/or C2InH of ≤ 2 mm. Narrow C2P was defined as C2P width ≤ 4 mm. STROBE checklist was followed. At least 1 HRVA was found in 25,3% (95% CI 21,1-29,8) of patients (16,7% of potential sites). At least 1 narrow C2P was seen in 36,8% (95% CI 32,1-41,7) of patients (23,8% of potential sites). Among those with HRVA, unilateral HRVA was present in 68,0% (95% CI 58,4-77,0), whereas bilateral HRVA in 32,0% (95% CI 23,0-41,6). No difference in terms of laterality (right or left) was seen neither for HRVA nor narrow C2P. Significant differences were found between females and males for all measurements. Each parameter showed either good or excellent inter- or intraobserver, and inter-software agreement coefficients. HRVA and narrow C2P are common findings in Central-European population and should be appreciated at the planning stage before craniocervical instrumentation. Measurements can be consistently reproduced by various observers at varying intervals using different software.