Suramin is a hexasulfonated naphthylurea commonly used as antitrypanosomial drug and for the treatment of malignant tumors. This compound has been recently characterized as a non-competitive thrombin inhibitor of activity over fibrinogen (Monteiro et al., Int J Biochem Cell Biol. 2004; 36, 2077-85), although the binding site on the enzyme were not determined. Herein, we have solved the crystal structure of the thrombin:suramin complex to 2.4 Å resolution, belonging to P2₁2₁2₁  space group. Thrombin-suramin interaction is mediated by several ionic, van-der-waals and hydrophobic contacts, including similar sulfate-protein contacts to that found in thrombin-heparin complexes. In fact, suramin interacts with a number of residues that constitute the thrombin heparin-binding exosite. Although a single thrombin:suramin complex was found per asymmetric unit, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. This crystallographic data support solution binding evidences of a ligand-bound dimer structure. Small angle X-ray scattering measurements were performed in order to obtain insights on the dimerisation behavior of thrombin upon suramin binding. We discuss the implications of dimmer formation in terms of the structural models obtained.