Background: The aim of this investigation was to compare skeletal and dentoalveolar measurements of subject with unilateral palatally impacted canine versus the unaffected contralateral side on cone beam computed tomography (CBCT). Methods: A cross-sectional study (split mouth design) that included 28 CBCTs (i.e., 56 sides) with unilaterally impacted maxillary canines was performed. After conducting a pilot test to gauge the researcher, heights and widths of skeletal and dentoalveolar variables obtained in the maxilla were measured using coronal and axial views. The angulations of incisors were also measured, and the side with impaction and the unaffected side were compared. Paired sample t test and Wilcoxon signed-rank test were used. Results: Significant statistical differences (2 mm, p < 0.001) were found between the impacted and non-impacted side measurements from the mid-palatine raphe to the first premolar (proximal alveolar bone crest between the canine (deciduous or permanent) and first premolar); the distance were significantly lower (12.72 ± 2.25 mm) than in the side without impaction (14.67 ± 2.00 mm). Also, the central and lateral incisor angulations showed significant reductions; presenting disto-angulated incisors on the impacted canine side (86.14 ± 7.70° and 74.75 ± 12.67°, respectively) and mesial-angulated incisors on the non-impacted side (91.63 ± 6.79° and 81.21 ± 8.56° respectively). The other skeletal and dentoalveolar measurements showed no significant differences. Conclusions: The width from the median raphe to the first premolar is lower in the side of maxillary palatal impacted canines than in the side without impaction. Lateral angulations of incisors were disto-angulated on the side of impacted canines. Both conditions have clinical implications in the orthodontic treatment.