During development, the extracellular matrix (ECM) is a complex dynamic structure whose components and organization help to establish the requisite position and state of differentiation. Until recently, the large chondroitin sulfate proteoglycan, aggrecan, has been localized predominantly to skeletal tissue and considered a hallmark of cartilage differentiation. We have identified the presence of aggrecan in two other highly differentiated systems, brain and notochord, with clearly distinct expression patterns. In chick cartilage, aggrecan starts to be expressed at embryonic day 5 in limb rudiments, continues through the entire period of chondrocyte development, and remains a biochemical marker of the cartilage phenotype thereafter. In brain, aggrecan has a very low level of expression beginning at day 7, increases up to day 13, markedly decreases after day 16, and is not expressed posthatching. This pattern coincides with migration and establishment of neuronal nuclei in the chick telencephalon and has been proposed to be a component of the migration arrest mechanism. In very primitive embryos, aggrecan is detected as early as stage 16 in the notochord, long before chondrogenesis occurs, is then expressed up to day 5 and decreases thereafter. The expression of aggrecan occurs during the time of active neural crest migration and through the onset of sclerotomal differentiation, and correlates with the notochords' ability to inhibit neural crest cell migration. Animal models defective in aggrecan biosynthesis have been invaluable in delineating these functions. In addition we have characterized these proteoglycans by chemical, biosynthetic, and molecular analyses. Although significant post-translation differences distinguish the cell-specific aggrecan species, their core proteins are the products of a single gene. Our findings of the expression of the same gene (aggrecan) in multiple ontogenously unrelated differentiating tissue systems and at different times over the developmental life of an organism provide an elegant model system to study the regulation and interplay in expression of that gene, as well as the effect of alterations in that single gene simultaneously in several developing programs.