Background: The application of three-dimensional computed tomography (3D CT) to analyse craniofacial morphology in individuals with cleft lip and palate (CLP) enables detailed assessments to be made of asymmetry in the region of the cleft and in regions distant from the cleft. The aim of this study was to compare craniofacial morphology in a sample of Malaysian infants with unoperated CLP with a control sample of unaffected Malaysian infants. Methods: The study sample comprised 29 individuals: 10 with unilateral CLP (UCLP), 5 with bilateral CLP (BCLP), 7 with cleft lip and primary palate (CLPP), and 7 with isolated cleft palate (ICP). The control sample consisted of 12 non-cleft (NC) infants. All subjects were between 0.4 and 12.2 months of age. Nine mid-facial and 4 nasal bone landmarks were located on 3D CT scans and compared to a midline reference plane, which was created using the landmarks basion, sella, and nasion. Unpaired t tests and F tests were used to compare means and variances between sample groups, whereas paired t tests were used for comparisons within the UCLP and NC groups. Results: Differences in variances of some mid-facial breadths and nasal bone dimensions were found in both male and female cleft groups when compared to the NC sample. In the UCLP group, some nasal bone and facial breadth dimensions were larger than in the NC sample and the nasal bone tended to deviate to the contralateral side of the cleft. Conclusion: : CLP affects the size and orientation of the nasal bones and is associated with an altered morphology of some facial bones at positions distant from the region of the cleft.