The properties of heparin and hirudin to inhibit thrombin from binding to the freshly-excised rabbit aorta wall were compared in vitro. When aorta segments were incubated with 125I-thrombin (4.4 ± 0.4 nM) in the presence of heparin or hirudin, both anticoagulants inhibited 125I-thrombin binding to the endothelium in a concentration-dependent manner (IC50: 0.1 USP U heparin/ml; 0.1 ATU hirudin/ml). Endothelium-bound 125I-thrombin was displaced by either heparin (50% liberated at 4.1 U/ml) or hirudin (0.4 U/ml). Using de-endothelialized aortas, heparin inhibited thrombin binding by the exposed subendothelium (IC50: 1.8 U/ml) whereas hirudin was without effect. Neither heparin nor hirudin was able to significantly liberate thrombin bound to the exposed subendothelium. These observations suggest that both heparin and hirudin mask the binding site on thrombin to the endothelial cell membrane. A separate site on thrombin must bind to the subendothelium because only heparin inhibits binding. Thrombin, although bound reversibly to the endothelium, is bound irreversibly to the exposed subendothelium due, probably, to reaction with endogenous extracellular antithrombin activities (e.g. antithrombin-III, protease nexin-1).