This work examines the validity of facial phenotypes as Autism Spectrum Disorders (ASD) biomarkers in boys with essential autism. A family-based association analysis framework is presented that uses previously identified facially-delineated (FD) clusters to examine relationship between FD clusters and known ASD genes. The hypothesis is that there are certain genetic variants, single nucleotide polymorphisms (SNP), specific to the FD clusters. Although statistical significance was not established, the results identified some candidate SNPs unique to each of the FD clusters that could indicate an underlying etiological difference. Further, recommendations are provided for larger-scale studies that could utilize the analysis framework presented.