Cleft lip and palate is the commonest congenital craniofacial anomaly and also affects the facial bones. In a unilateral cleft lip and palate (UCLP), there is asymmetry in the mid-face and also within the maxilla between the cleft and non-cleft sides. The aim of this study is to develop a 3-dimensional model of an UCLP skull from a patient's cone-beam computed tomography and measure the asymmetry. The model is constructed with manual segmentation of all regions using MIMICS v14.0 and measurements were done by 3-matic software. Measurements in the mid-face and maxilla were carried out in all planes of interest. Asymmetry was present not only in the maxilla but extends to the orbital, zygomatic, and frontal bones. Through this methodology and model, asymmetric variations <0.5 mm could be assessed precisely thus having potential applications in treatment planning of craniofacial deformities.