The parental craniofacial morphology in orofacial clefting (OFC) has been shown to differ from that of the non-cleft population when evaluated using conventional cephalometric analyses comprising a variety of linear, angular, and area measurements. In spite of this, the shape of the parental craniofacial complex is of greater importance in the search for the morphogenes involved in OFC. This retrospective case–control study employed three morphometric techniques [discriminant analysis of the principal components of shape (PCS), Euclidean distance matrix analysis (EDMA), and thin-plate spline analysis (TPS)] to localize the craniofacial skeletal shape differences between (a) the parents of children with OFC and a comparison group, (b) the parents of children with cleft lip and palate [CL(P)] and cleft palate (CP), and (c) the male and female parents of children with OFC. The postero-anterior (PA) cephalograms of 92 parents of children with non-syndromic OFC and 43 comparison group volunteers were scanned and digitized. The configurations of 24 reproducible landmarks were optimally superimposed using Procrustes algorithms to allow shape data to be derived using PCS, EDMA, and TPS. The parental craniofacial shape statistically significantly differed from that of the comparison group using PCS (P < 0.001) and EDMA (P = 0.001). However PCS, EDMA, and TPS differed in their localization of the shape differences, explainable by the different mathematical methods used by the individual techniques. Interestingly, the parental craniofacial shapes in CL(P) and CP were morphologically similar when tested using PCS (P = 0.03) and EDMA (P = 0.027). However, there was no shape-related sexual dimorphism in parental craniofacial morphology in OFC when tested using PCS (P = 0.35) and EDMA (P = 0.525). Thus, the parental craniofacial shape in OFC differs from the non-cleft population, the parental craniofacial shape does not differ between CL(P) and CP and there is no sexual dimorphism in the parental craniofacial morphology in OFC, as viewed on PA cephalograms.