Heparan sulfate (HS) binds and modulates the transport and activity of a large repertoire of regulatory proteins. The HS phage display antibodies are powerful tools for the analysis of native HS structure in situ; however, their epitopes are not well defined. Analysis of the binding specificities of a set of HS antibodies by competitive binding assays with well defined chemically modified heparins demonstrates that O-sulfates are essential for binding; however, increasing sulfation does not necessarily correlate with increased antibody reactivity. IC 50 values for competition with double modified heparins were not predictable from IC 50 values with corresponding singly modified heparins. Binding assays and immunohistochemistry revealed that individual antibodies recognize distinct epitopes and that these are not single linear sequences but families of structurally similar motifs in which subtle variations in sulfation and conformation modify the affinity of interaction. Modeling of the antibodies demonstrates that they possess highly basic CDR3 and surrounding surfaces, presenting a number of possible orientations for HS binding. Unexpectedly, there are significant differences between the existence of epitopes in tissue sections and observed in vitro in dot blotted tissue extracts, demonstrating that in vitro specificity does not necessarily correlate with specificity in situ/ vivo. The epitopes are therefore more complex than previously considered. Overall, these data have significance for structure-activity relationships of HS, because the model of one antibody recognizing multiple HS structures and the influence of other in situ HS-binding proteins on epitope availability are likely to reflect the selectivity of many HS-protein interactions in vivo.HS 2 belongs to the glycosaminoglycan family of polysaccharides and can be considered the most information-rich biopolymer in nature. HS chains consist of repeating -D-glucuronic acid and GlcNAc units, which are subject to enzymatic postpolymeric modification by N-deacetylation and N-sulfation of GlcNAc, O-sulfation at various positions, and epimerization of D-glucuronic acid to its C-5 epimer, iduronic acid. HS biosynthetic enzymes do not act upon every potential site within a chain, resulting in chains with a high level of structural diversity and a distinct domain structure, with regions of unmodified saccharides (N-acetyl domains) and highly modified saccharides (N-sulfated domains) flanked by regions of alternating modified and unmodified disaccharides (transition or N-acetyl/ N-sulfated domains) (1-4). HS chains are usually attached to core proteins, forming HS proteoglycans, and these proteoglycans represent one of the major components of most metazoan cell surfaces and extracellular matrices. Here, they control cellcell and cell-matrix communication by association with a large repertoire of regulatory proteins (5), including growth factors, morphogens, extracellular matrix components, enzymes, cell adhesion molecules, and cytokines. It is through these int...