The CC chemokine macrophage inflammatory protein 1alpha (MIP1alpha) is a key regulator of the proliferation and differentiation of hematopoietic progenitor cells. The activity of MIP1alpha appears to be modulated by its binding to heparan sulfate (HS) proteoglycans, ubiquitous components of the mammalian cell surface and extracellular matrix. In this study we show that HS has highest affinity for the dimeric form of MIP1alpha. The predominantly dimeric BB10010 MIP1alpha interacts with an 8.3-kDa sequence in the HS polysaccharide chain, which it protects from degradation by heparinase enzymes. The major structural motif of this HS fragment appears to consist of 2 sulfate-rich S-domains separated by a short central N-acetylated region. The optimum lengths of these S-domains seem to be 12 to 14 saccharides. We propose that this binding fragment may wrap around the MIP1alpha dimer in a horseshoe shape, facilitating the interaction of the S-domains with the heparin-binding domains on each monomer. Molecular modeling suggests that these S-domains are likely to interact with basic residues Arg 17, Arg 45, and Arg 47 and possibly with Lys 44 on MIP1alpha and that the interconnecting N-acetylated region is of sufficient length to allow the 2 S-domains to bind to these sites on opposite faces of the dimer. Elucidation of the structure of the HS-binding site for MIP1alpha may enable us to devise ways of enhancing its myeloprotective or peripheral blood stem cell mobilization properties, which can be used to improve cancer chemotherapy treatments.