Objective: This study was performed to investigate the changes in alveolar bone after maxillary incisor intrusion and to determine the related factors in deep-bite patients. Methods: Fifty maxillary central incisors of 25 patients were evaluated retrospectively. The maxillary incisors in Group I (12 patients; mean age, 16.51 +/- 1.32 years) were intruded with a base-arch, while those in Group II (13 patients; mean age, 17.47 +/- 2.71 years) were intruded with miniscrews. Changes in the alveolar envelope were assessed using pre-intrusion and post-intrusion cone-beam computed tomography images. Labial, palatal, and total bone thicknesses were evaluated at the crestal (3 mm), midroot (6 mm), and apical (9 mm) levels. Buccal and palatal alveolar crestal height, buccal bone height, and the prevalence of dehiscence were evaluated. Two-way repeated measure ANOVA was used to determine the significance of the changes. Pearson's correlation coefficient analysis was performed to assess the relationship between dental and alveolar bone measurement changes. Results: Upper incisor inclination and intrusion changes were significantly greater in Group II than in Group I. With treatment, the alveolar bone thickness at the labial bone thickness (LBT, 3 and 6 mm) decreased significantly in Group II (p < 0.001) as compared to Group I. The LBT change at 3 mm was strongly and positively correlated with the amount of upper incisor intrusion (r = 0.539; p = 0.005). Conclusions: Change in the labial inclination and the amount of intrusion should be considered during upper incisor intrusion, as these factors increase the risk of alveolar bone loss.