ObjectiveThis study aimed to assess the alveolar bone changes following maxillary and mandibular molars’ intrusion and extrusion movements using Clear Aligners using Cone-Beam Computed Tomography (CBCT).Materials and methodsThis is a retrospective clinical study in which 24 adult patients with pre-designed selection criteria and a mean age of 31.1 + 9.9 years were enrolled. The alveolar bone changes around one hundred thirty-three maxillary and mandibular molars intruded or extruded by Clear Aligners therapy were analyzed from CBCT using Invivo 6.0 software. Intra- and inter-examiner reliability analysis was performed using the intra-class correlation coefficient (ICC) and Cronbach’s Alpha statistics. The paired t-test was used to analyze significant differences before and after treatment (T0-T1). The significance level was considered at P < 0.05.ResultThe patients were divided into two groups: extrusion (48.9%, n = 65 molars’ root) and intrusion (51.1%, n = 68 molars’ root) group. There was a significant decrease in the alveolar bone changes in the buccal surface of the mandibular right and left 1st molars in the extrusion group (-1.05 ± 0.97, -0.76 ± 1.12 mm, respectively) and the maxillary left 2nd molars in intrusion group (-0.42 ± 0.77 mm), and the lingual surface of intrusion of the mandibular left 1st molar (-0.64 ± 0.76 mm). Comparing the mean maxillary and mandibular changes (T0-T1) of both studied groups showed that the buccal alveolar bone changes for the left 1st and right 2nd molars showed a significant difference in extrusion and intrusion groups, respectively.ConclusionsThe buccal alveolar bone changes is considered the most affected surface following maxillary and mandibular molars’ intrusion and extrusion movements using clear aligners, with mandibular molars being more affected than the maxillary ones.