Introduction: The nasal septum, a component of the chondrocranium, acts as a growth center that may have a morphogenetic influence on adjacent intramembranous-derived structures of the nasofacial complex. Recent evidence has demonstrated that morphological variation in the nasofacial complex is potentially due to early developmental variation in chondrocranial-derived nasal structures. There are likely both local and systemic factors that affect inter-population nasal variation. If the morphology of the nasal complex is driven, at least in part, by the morphogenetic effects of cartilage during ontogeny, then selection for altered nasal morphology under different climatic conditions is potentially achieved via developmental changes in chondrocranial-derived structures. This suggests that genes influencing the development of cartilage-derived structures may be the targets of climate-mediated selection. The purpose of this study is to further examine the potential influence of variation in chondrocranial-derived structures on gross nasal morphology by utilizing a candidate gene approach to assess phenotype/genotype associations in the nasal complex. Materials and methods: Using cone beam computed tomography scans (CBCT), we collected a series of k=44 landmarks representing different cartilaginous and osseous nasal components from an adult sample (n = 120). A group of 69 loci from 22 genes were selected that have been previously found to have an association to cartilage development or variation in the nasal complex in humans and animal models. Centroid size of coordinate landmark configurations were used to quantify nasal complex size. A principle components analysis was used to quantify nasal complex shape. Phenotypes were characterized using the symmetric component of variation. Subjects were categorized by genotype for each SNP (i.e., AA, AB, BB) analyzed, and significant differences in PC scores were tested using ANOVA. Results: There were no significant associations between nasal complex size and genotype for any of the SNPs analyzed. Phenotype/genotype relationships were assessed for the first four PCs, which accounted for 47.89% of the total variation in the sample. Significant associations between individual PC scores and genotypes were found. Conclusion: Our results indicate that nasal complex variation is associated with a number of genes that have been previously linked to skeletal tissue development and facial morphogenesis.