Introduction The purpose of this study was to compare the transverse, vertical, and anteroposterior skeletal and dental changes in adolescents receiving expansion treatment with tooth-borne and bone-anchored expanders. Immediate and long-term changes were measured on cone-beam computed tomography (CBCT) images. Methods Sixty-two patients needing maxillary expansion were randomly allocated to 1 of 3 groups: traditional hyrax tooth-borne expander, bone-anchored expander, and control. CBCT images were taken at baseline, immediately after expansion, after removal of the appliance (6 months), and just before fixed bonding (12 months). Repeated measures multivariate analysis of variance (MANOVA) was applied to the distances and angles measured to determine the statistical significance in the immediate and long time periods. Bonferroni post-hoc tests were used to identify significant differences between the treatment groups. Results Immediately after expansion, the subjects in the tooth-borne expander group had significantly more expansion at the crown level of the maxillary first premolars (P = 0.003). Dental crown expansion was greater than apical expansion and skeletal expansion with both appliances. The control group showed little change (growth) over the 6-month interval. At 12 months, no group had a statistically significant difference in angle changes, suggesting symmetric expansion. Both treatment groups had significant long-term expansion at the level of the maxillary first molar crown and root apex, first premolar crown and root, alveolus in the first molar and premolar regions, and central incisor root. Tooth-borne expansion resulted in significantly more long-term expansion at the maxillary premolar crown and root than did bone-borne expansion. Conclusions Both expanders showed similar results. The greatest changes were seen in the transverse dimension; changes in the vertical and anteroposterior dimensions were negligible. Dental expansion was also greater than skeletal expansion. The purpose of this study was to compare the transverse, vertical, and anteroposterior skeletal and dental changes in adolescents receiving expansion treatment with tooth-borne and bone-anchored expanders. Immediate and long-term changes were measured on cone-beam computed tomography (CBCT) images. Sixty-two patients needing maxillary expansion were randomly allocated to 1 of 3 groups: traditional hyrax tooth-borne expander, bone-anchored expander, and control. CBCT images were taken at baseline, immediately after expansion, after removal of the appliance (6 months), and just before fixed bonding (12 months). Repeated measures multivariate analysis of variance (MANOVA) was applied to the distances and angles measured to determine the statistical significance in the immediate and long time periods. Bonferroni post-hoc tests were used to identify significant differences between the treatment groups. Immediately after expansion, the subjects in the tooth-borne expander group had significantly more expansion at the crown level of the maxillary first premolars (P = 0.003). Dental crown expansion was greater than apical expansion and skeletal expansion with both appliances. The control group showed little change (growth) over the 6-month interval. At 12 months, no group had a statistically significant difference in angle changes, suggesting symmetric expansion. Both treatment groups had significant long-term expansion at the level of the maxillary first molar crown and root apex, first premolar crown and root, alveolus in the first molar and premolar regions, and central incisor root. Tooth-borne expansion resulted in significantly more long-term expansion at the maxillary premolar crown and root than did bone-borne expansion. Both expanders showed similar results. The greatest changes were seen in the transverse dimension; changes in the vertical and anteroposterior dimensions were negligible. Dental expansion was also greater than skeletal expansion.