Heparan sulfate proteoglycans (HSPGs) at the cell surface and in the extracellular matrix have important functions during embryonic development. They act as essential coreceptors and their interaction with various exogenous factors allows the generation and maintenance of morphogen gradients. The sulfation pattern of the heparan sulfate (HS) side chains, deciding the factors that will bind and the affinity of the interaction, is determined largely during biosynthesis. In addition, after biosynthesis, the HS chains may be modified by the endo-6-O-sulfatases (Sulf 1 and 2, see below) or by heparanase, an endo-glycosidase that generates HS fragments. Biosynthesis occurs in the Golgi compartment and involves the action of several different enzymes, some of which occur in more than one isoform. The enzymes that will be mostly discussed here are Ext1, which, together with Ext2, forms the functional HS polymerase, and the glucosaminyl N-deacetylase/sulfotransferases (Ndsts), which are responsible for the HS N-sulfation that controls the subsequent enzymatic reactions, thereby affecting the overall structure of HS chains. Biosynthesis of HS is covered in two companion mini-reviews (Kreuger & Kjellén 2012;Multhaupt and Couchman 2012).HS is essential for animal development, as evidenced by mutational studies in model organisms, including Drosophila melanogaster, mouse, Caenorhabditis elegans and zebrafish. In the mouse, complete interruption of HS biosynthesis by obliteration of the polymerases, Ext1 or Ext2 (Lin et al. 2000;Stickens et al. 2005), led to early termination of mouse embryonic development. Selected elimination of the enzymes involved in modification of HS structure resulted in strikingly varied phenotypes in mice. Inhibition of N-sulfation by 465090J HCXXX10.1369/0022155412465090Tamm et al.Heparan Sulfate Biosynthesis Enzymes in Embryonic Stem Cell Biology 2012© The Author(s) 2010 Reprints and permission