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To investigate the accuracy of O-arm navigation-assisted screw insertion in extremely small thoracic pedicles and to compare it with free-hand pedicle screw insertion in adolescent idiopathic scoliosis (AIS).A total of 344 pedicle screws were inserted in apical region (defined as 2 vertebrae above and below the apex each) of 46 AIS patients (age range 13–18 years) with O-arm navigation and 712 screws were inserted in 92 AIS patients (age range 11–17 years) with free-hand technique. According to the narrowest diameter orthogonal to the long axis of the pedicle on a trajectory entering the vertebral body on preoperative computed tomography, the pedicles were classified into large (>3 mm) and small (≤3 mm) subgroups. Furthermore, a subset of extremely small pedicles (≤2 mm in the narrowest diameter) was specifically discussed. Screw accuracy was categorized as grade 0: no perforation, grade 1: perforation by less than 2 mm, grade 2: perforation by 2 to 4 mm, grade 3: perforation over 4 mm.In the O-arm group, the mean thoracic pedicle diameters were 2.23 mm (range 0.7–2.9 mm) and 3.48 mm (3.1–7.1 mm) for small and large pedicles, respectively. In the free-hand group, the small and large thoracic pedicle diameters were 2.42 mm (range 0.6–2.9 mm) and 3.75 mm (3.1–6.9 mm), respectively. The overall accuracies of screw insertion in large and small thoracic pedicles (grade 0, 1) were significantly higher in O-arm group (large: 93.8%, 210/224, small: 91.7%, 110/120) than those of free-hand group (large: 84.9%, 353/416, small: 78.4%, 232/296) (P < 0.05). Importantly, the overall accuracy of screw placement in extremely small pedicles was significantly higher in the O-arm group (84.3%, 48/57) compared with 62.7% (79/126) in free-hand group (P < 0.05), and the incidence of medial perforation was significantly lower in O-arm group (11.1%, 1/9) compared with 17.0% (8/47) in free-hand group (P < 0.05).The O-arm intraoperative navigation system should be acknowledged for its superiority in scoliosis surgery, since it permits more accurate and safer instrumentation for AIS patients with small and extremely small thoracic pedicles.