Vascular injury, activation of the coagulation system and thrombosis are common initial events in the accelerated atherosclerotic process. The role of thrombin generated at the site of aortic injury in the subsequent neointimal proliferation was studied in rabbits (n = 16) 3 weeks after balloon catheter injury. In half of these animals, potent thrombin antagonists, r-hirudin and P-PACK, were administered to prevent acute thrombotic events. Compared to aortas with intact endothelium (n = 8), aortas de-endothelialised 21 days earlier showed neointimal hyperplasia as measured by the intimal/medial ratio (0.68 vs. 0.04, injured vs. normal aortas) and an increase in both total cholesterol (4.08 vs. 3.31 mg/g, p < 0.05) and lipid peroxide content (31.3 vs. 1.1 nmol/g; p < 0.001). Neointimal hyperplasia following endothelial denudation was inhibited in rabbits treated with thrombin-antagonists (0.27 vs. 0.68, treated vs. untreated, p = 0.012) and neither total cholesterol (3.48 mg/g) nor lipid peroxide content (1.5 nmol/g) differed significantly from that of intact arteries. By demonstrating a strong relationship between thrombin generation following de-endothelialisation and the progressive intimal proliferation, this study supports the hypothesis that thrombin is an important contributor to restenosis after vascular injury. The highly atherogenic lipid peroxidation seems to be linked to the early, thrombin-mediated events, as it was completely prevented by adequate thrombin antagonism.