BACKGROUND: Specificity in leukocyte trafficking is likely to depend on sequential interactions between various cell-type-specific leukocyte adhesion molecules, such as selectins and integrin ligands, and leukocyte-activating factors. A major class of leukocyte-activating factors, the chemokines, are soluble polypeptides that bind glycosaminoglycans, the polysaccharide components of cell-surface and extracellular-matrix proteoglycans. It has been suggested that cell-surface glycosaminoglycans of the heparin/heparan sulfate class mediate the presentation of chemokines to leukocytes by vascular endothelial cells. We investigated the possibility that specificity exists in the recognition of particular heparin/heparan sulfate structures by chemokines, by studying the binding of four members of the chemokine superfamily to heparin and heparan sulfate. RESULTS: Using affinity co-electrophoresis we found that interleukin-8 preferentially bound a subfraction of heparin that also showed increased affinity for melanoma growth stimulating activity (also known as MGSA, GRO or GRO alpha). This same subfraction of heparin, however, was not significantly preferentially bound by platelet factor 4 or neutrophil activating factor-2. Subsequent analysis of the three-dimensional structures of these chemokines indicated that their ability to discriminate among heparin subspecies correlates with the presence of paired glutamic acid residues within the putative glycosaminoglycan-binding site of the chemokine. This observation led to predictions about the relative affinities of heparan sulfate for interleukin-8 and platelet factor 4, predictions that were confirmed by further binding assays. CONCLUSION: Chemokines can bind selectively to subsets of heparin/heparan sulfate glycosaminoglycans, raising the possibility that glycosaminoglycans participate in determining the specificity of leukocyte recruitment in vivo.