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Objective: To investigate the discrepancy of crown-root morphology of upper and lower central incisors in adult patients with different skeletal malocclusions using cone-beam CT (CBCT). Methods: Patients visiting the Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University from January 2015 to December 2017 were selected, including 108 cases (52 males, 56 females, aged from 18 to 30 years, mean age 25.8 years). According to CBCT data and cephalometric analysis, 66 patients with average angle were selected as the sagittal skeletal group, including 24 Class Ⅰ patients, 20 Class Ⅱ and 22 Class Ⅲ patients. In the other selected 66 skeletal Class Ⅰ patients including 21 low angle patients, 24 average angle patients (from the sagittal skeletal Class Ⅰ subgroup) and 21 high angle patients. Invivo 5 software was used to locate the CBCT image three dimensionally and then obtain the middle labio-lingual section of right central incisor. Auto CAD 2007 software was applied to measure the angle formed by the long axis of root and the extension line of the long axis of crown (Collum angle), and the angle between the long axis of crown and the lip tangent line passing through the center of the labial surface of crown (labial surface angle). One-way ANOVA and Scheff were used to analyze the discrepancies among classifications and Pearson correlation analysis was used to determine the correlation between the Collum angles and labial surface angles. Results: Significant differences were found in Collum angles and labial surface angles among different sagittal skeletal patterns ( P< 0.05). The Collum angle of maxillary central incisors in Class Ⅱ patients was 5.18°±4.97° and the average labial surface angle was 17.78°±3.74°, which were both significantly higher than that of maxillary central incisors in Class Ⅰ and Ⅲ subgroups ( P< 0.05). Similarly, the above two angles of mandibular central incisors in Class Ⅲ were 5.59°±5.64° and 15.32°±3.05°, which were significantly higher than that of mandibular central incisors in Class Ⅰ and Ⅱ subgroups ( P< 0.05). There was no significant difference among different vertical skeletal patterns ( P> 0.05). Notably, the Collum angles of maxillary or mandibular central incisors presented significantly positive correlation with labial surface angles (maxillary: r= 0.723, P <0.001; mandibular: r= 0.752, P <0.001). Conclusions: The long axis of the crown of the maxillary central incisor in skeletal Class Ⅱ patients and the mandibular central incisor in skeletal Class Ⅲ patients are obviously deviated toward the lingual side relative to the long axis of the root, and correspondingly there is a greater labial surface angle of the crown, which indicates that equivalent positioning deviation during bracket bonding can cause greater torque expression error.