Unilateral cleft lip and palate (UCLP) occurs when the maxillary and nasal facial prominences fail to fuse correctly during development, resulting in a palatal cleft and clefted soft and hard tissues of the dentoalveolus. The UCLP deformity may compromise an individual's ability to eat, chew, and speak. In this retrospective cross-sectional study, cone beam computed tomography (CBCT) images of 7-17-year-old individuals born with UCLP (n = 24) and age- and sex-matched controls (n = 24) were assessed. Coordinate values of three-dimensional anatomical landmarks (n = 32) were recorded from each CBCT image. Data were evaluated using principal coordinates analysis (PCOORD) and Euclidean distance matrix analysis (EDMA). Approximately 40% of morphometric variation is captured by PCOORD axes 1-3, and the negative and positive ends of each axis are associated with specific patterns of morphological differences. Approximately 36% of facial skeletal measures significantly differ by confidence interval testing (α = 0.10) between samples. Although significant form differences occur across the facial skeleton, strong patterns of morphological differences were localized to the lateral and superioinferior aspects of the nasal aperture, particularly on the clefted side of the face. The UCLP deformity strongly influences facial skeletal morphology of the midface and oronasal facial regions, and to a lesser extent the upper and lower facial skeletons. The pattern of strong morphological differences in the oronasal region combined with differences across the facial complex suggests that craniofacial bones are integrated and covary, despite influences from the congenital cleft.