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Inaccurate identification of vertebral levels is the main cause of wrong-site spine surgery which is performed by nearly half of the spine surgeons. Unusual anatomy and failure to verify the surgical level on radiographs have been commonly reported. We aimed at investigating the variations in vertebral number in adolescent idiopathic scoliosis (AIS) patients and thus to raise awareness of the possibility for wrong-level spinal surgery and to make a comparison with normal adolescents. A cohort of 657 AIS patients and 248 normal adolescents, presented to our center from June 2008 to February 2013, who met the inclusion criteria, were recruited. Radiographs were reviewed to identify the number of thoracic or lumbar vertebrae and the presence of a lumbosacral transitional vertebra. In the AIS group, 70 (10.6%) patients had variations in the number of thoracic and/or lumbar vertebrae. Remarkably, the prevalence of variations in male subjects was significantly higher than that in female subjects (P < 0.05). Thirty-seven patients (5.6%) had an atypical number of thoracic vertebrae, with 33 having 11 thoracic vertebrae and 4 patients having 13. Forty-eight patients (7.3%) had an atypical number of lumbar vertebrae, with 14 having 4 lumbar vertebrae and 34 patients having 6. Multilevel vertebral anomalies were present in 2.3% of the patients (15 of 657). A variation in the number of vertebrae had been identified in 1.7% (11) of the reports by the radiologist. In the normal group, 27 (10.9%) subjects showed variations in the vertebral number. There was no significant difference in the prevalence of atypical numbers of vertebral number between the AIS and normal groups (P > 0.05). Therefore, we concluded that variations in the number of thoracic–lumbar vertebrae were found in up to10.6% of AIS patients. Identification of variations in the number of vertebrae is crucial to serve to decrease the risk of wrong-level surgery.