Heparin is a widely prescribed anticoagulant that has been in clinical use for over 70 years. It is a natural product and a special form of heparan sulfate, a heterogeneous polysaccharide that is expressed as a proteoglycan on the surface of all animal tissues. In recent years, the development of a chemoenzymatic method to synthesize specific heparan sulfate polysaccharides and oligosaccharides has enabled studies of the structure-based interactions between negatively charged heparan sulfate and its protein binding partners. A synthetic version of heparin and its low-molecular-weight derivatives could have several advantages over the drugs that are currently available. First, a synthetic drug would evade the historically contaminated porcine intestine supply chain from which heparin is currently derived. In addition, the structure of the drug could be tailored for improved safety and efficacy and to meet the needs of different patient populations. In this dissertation, we sought to characterize structure-function relationships of heparan sulfate with several goals: to reduce binding to platelet factor 4, an initiating step in heparin-induced thrombocytopenia; to identify the structure required for binding to Stabilin receptors, which clear heparins via the liver rather than the kidneys; and to create a heparan sulfate structure that has optimum bioavailability and activity against factors of the coagulation cascade. Through biochemical, cell-based and in vivo assays, we determined that PF4 binding was decreased by Sulf-2 treatment and by limiting the oligosaccharide length, that a 3-O-sulfated 10-mer is required for robust Stabilin binding, that a 19-mer will confer anti-IIa activity and that oligosaccharides as short as a 6-mer are bioavailable through subcutaneous injection.