Proteoglycan core proteins are linked to four different classes of linear sugar chains referred to as glycosaminoglycans. Heparan sulfate constitutes one of these classes of glycosaminoglycans, and has been shown to be important in developmental processes as well as disease. We designed a low-density gene expression array to identify expression levels of heparan sulfate biosynthetic enzymes and proteoglycan core proteins in the aorta of late stage embryos (E18.5) and adult mice (12 weeks). Significant changes were found in mRNA expression of proteoglycan core proteins syndecan, glypican, decorin, perlecan, and versican from development to adulthood (n = 8, p < 0.05). Immunohistochemistry revealed a striking localization of both decorin and perlecan staining to the subendothelium in adult vessels, which differed from consistent staining of the endothelium, smooth muscle, and adventitia in development. Significant differences were also identified in the expression of the heparan sulfate modifying enzymes, glururonyl C5 epimerase, 2-O and 6-O sulfotransferases, and N-deacetylase/N sulfotransferases 1-3 (n = 8, p < 0.05). In conclusion, proteoglycan core proteins and heparan sulfate biosynthetic enzymes in the aorta undergo significant changes in their expression from development to adulthood. These findings may have important biological significance in the specific cell-defined roles of proteoglycan and heparan sulfate related targets in vascular development, maintenance, and response to various perturbations.