Background: The aim of the present study was to assess the degree of apical vertebral rotation values in Adolescent Idiopathic Scoliosis (AIS) that were obtained on CT scans, and to analyze the influence of patient position (supine versus prone) on the degree of rotation. Methods: The study included 50 apical vertebra rotation measurements of 34 patients with Type 1A and Type 3C curvature according to the Lenke classification. CT imaging was applied to the patients in supine and prone positions to measure the apical vertebral rotation (AVR). The average AVR angles were measured using the Aaro–Dahlborn method and the results were compared. Results: No significant differences were found between the vertebral rotation measured in the prone and supine positions for the Lenke 1A subgroup and the Lenke 3C thoracic group (p = 0.848; p = 0.659, respectively). In the Lenke 3C lumbar group, however, the vertebral rotation in the supine position was found to be significantly lesser than that in the prone position (difference −1.40° ± 1.79°, p = 0.007). Conclusion: The assessment of the apical vertebra rotation is crucial in AIS. Even though the vertebral rotation in the supine position was found to be significantly lesser than that in the prone position, CT imaging in a prone position could not be considered clinically more relevant than the CT images in a supine position as there was less than 3° difference.