The precise role that genes play in early craniofacial development and postnatal craniofacial growth are essential to understand dento-facial development overall. However, genotype-phenotype correlations between genetic variation of early craniofacial genes and adult craniofacial phenotypes is poorly understood. Thus, this thesis focused on identifying the genetic etiology underlying phenotypic variations present in malocclusion conditions. First, we performed genotype-phenotype association analyses between common variants in 82 craniofacial genes and phenotypic variations extracted from 2D and 3D pre-treatment dental records of individuals with malocclusion. This effort identified that variant rs2189000 upstream of TWIST1 is highly associated with mandibular body length and inclination and cranial base angulations which can lead to malocclusion. Next, via cell based functional assays, we discovered that rs2189000 disrupts a PITX2 binding site and also showed the direct regulation of TWIST1 expression by the PITX2 gene. Finally, we identified abnormal craniofacial phenotypes and malocclusion in Twist1 deleted mice including asymmetric snouts, domed cranial vaults, and changes in size and inclination of the cranial base, palate and mandible resulting in malocclusion and resembling the human phenotypes observed. Also, premature calcification of calvarial sutures and cranial base synchondroses were also observed in the mutant mice indicating a possible biological mechanism for the abnormal phenotypes detected. These results confirm that TWIST1 is an important regulator of postnatal growth and that genetic variation in TWIST1 can result in malocclusion. The continued identification of genetic etiological factors and their role in craniofacial growth will impact treatment and prevention of malocclusion and other craniofacial conditions