Indiana University-Purdue University Indianapolis (IUPUI) / Trisomy 21 occurs in approximately 1 out of 750 live births and causes brachycephaly, a small oral cavity, a shortened mid-face, and mental impairments in individuals with Down syndrome (DS). Craniofacial dysmorphology occurs in essentially all individuals with trisomy 21 and causes functional difficulties. Mouse models are commonly used to study the etiology of human disorders because of the conserved phenotypes between species. The Ts65Dn Down syndrome mouse model has triplicated homologues for approximately half the genes on human chromosome 21 and exhibits many phenotypes that parallel those found in individuals with DS. Specifically, newborn and adult Ts65Dn mice display similar craniofacial defects as humans with DS. Ts65Dn embryos also exhibit smaller mandibular precursors than their euploid littermates at embryonic day 9.5 (E9.5). Furthermore, Ts65Dn mice exhibit reduced birth weight which suggests a possible generalized delay in overall embryonic growth. Based on previous research at E9.5, it was hypothesized that Ts65Dn E13.5 embryos would have reduced mandibular precursors with altered gene expression. It was also hypothesized that other neural crest derived structures would be reduced in trisomic embryos. Using morphological measurements it was determined that the mandible, Meckel’s cartilage, and hyoid cartilage were significantly reduced in E13.5 trisomic embryos. The tongue was of similar size in trisomic and euploid embryos while cardiac and brain tissue volumes were not significantly different between genotypes. Analysis of total embryonic size at E9.5 and E13.5 revealed smaller trisomic embryos with developmental attenuation that was not related to maternal trisomy. A microarray analysis performed on the mandibular precursor revealed 155 differentially expressed non-trisomic genes. Sox9 was of particular interest for its role in cartilage condensation and endochondral ossification. It was hypothesized that the overexpression of Sox9 in the developing mandible would be localized to Meckel’s and hyoid cartilages. Immunohistochemistry performed on the mandibular precursor confirmed an overexpression of Sox9 in both Meckel’s and the hyoid cartilages. This research provides further insight into the development of trisomic tissues, both neural crest and non-neural crest-derived, and also the specific molecular mechanisms that negatively affect mandibular development in Ts65Dn mice and presumably individuals with Down syndrome.