Heparan sulfate is a sulfated glycan that exhibits essential physiological functions, and heparin is a clinically used anticoagulant drug. Interrogation of the specificity of heparan sulfate-mediated activities demands a library of structurally defined oligosaccharides. Synthesis of heparan sulfate using enzymes provides a promising approach because of the high regioselectivity of heparan sulfate biosynthetic enzymes. The synthesis of heparan sulfate involves 15 different enzymes, including sulfotransferases, an epimerase and glycosyltransferases. Up to now, a number of oligosaccharides with different sulfation patterns and sizes were synthesized. These oligosaccharides are now used to probe the biosynthetic mechanism of heparan sulfate and heparin, improving the synthesis of heparin drugs, and understanding the interaction of heparan sulfate with proteins. The availability of structurally defined heparan sulfate oligosaccharides will significantly advance the ability to understand the biology of heparan sulfate.