Pluripotent embryonic stem cells (ESCs) must select between alternative fates of self-renewal and lineage commitment at each division during continuous proliferation. Heparan sulfate (HS) is a highly sulfated polysaccharide and is present abundantly on the ESC surface. In this study, we investigated the role of HS in ESC self-renewal by examining Ext1 ؊/؊ ESCs that are deficient in HS. We found that Ext1 ؊/؊ ESCs retained their self-renewal potential but failed to transit from self-renewal to differentiation upon removal of leukemia inhibitory factor. Furthermore, we found that the aberrant cell fate commitment is caused by defects in fibroblast growth factor signaling, which directly retained high expression of the pluripotency gene Nanog in Ext1 ؊/؊ ESCs. Therefore, our studies identified and defined HS as a novel factor that controls ESC fate commitment and also delineates that HS facilitates fibroblast growth factor signaling, which, in turn, inhibits Nanog expression and commits ESCs to lineage differentiation.Embryonic stem cells (ESCs) 2 are derived from the inner cell mass of the preimplantation blastocyst and can differentiate into numerous cell types representative of all three germ layers of the embryo, a property that is defined as pluripotency (1, 2). ESCs retain pluripotency through a process of self-renewal, which allows ESCs to proliferate infinitely as undifferentiated entities. These properties make ESCs a unique system to study early embryonic development and cell fate decisions and provide us with a promising source for cell replacement therapies (3-5). The regulatory network and molecular requirements for the maintenance of self-renewal have been under intense investigation and are now increasingly defined. However, the mechanisms by which ESCs exit the self-renewing state and initiate differentiation are still poorly understood. For example, recent reports suggest that extrinsic signaling of fibroblast growth factors (FGFs) and intracellular factors, including the chromatin-associated protein UTF1 (undifferentiated embryonic cell transcription factor 1) and the nucleosome remodeling complex, NuRD, are instrumental in triggering the exit of ESCs from their self-renewal program and to commit to differentiation (6 -8).Heparan sulfate (HS) is a highly sulfated glycosaminoglycan molecule and is biosynthesized in the Golgi apparatus of cells (9, 10). The copolymerases EXT1 and EXT2 initiate HS biosynthesis by alternately adding glucuronic acid and Nacetylglucosamine residues to form HS precursors. Following chain elongation, N-deacetylase/N-sulfotransferases act on discrete regions of the HS precursors, replacing N-acetyl groups with N-sulfate and creating appropriate substrates for further modification reactions, including epimerization and O-sulfation. The modification reactions are incomplete and result in mature HS that is structurally highly heterogeneous and possesses the potential to interact with a large variety of protein ligands. In tissues, the HS chains covalently attach to core prote...