Objective: To observe the effects of different doses of urokinase, given at different times after thrombus formation, on the vascular wall of the affected vessels in rats with deep vein thrombosis (DVT). Methods: Ninety-six SD rats were equally randomized into stage I, stage II, stage III and stage IV groups according to the time elapsed since thrombus formation (1, 3, 7, and 14 d) after the establishment of DVT model. The rats of each stage group were equally randomized again into model group, low-dose urokinase [20 000 U/(kg?d)] group, mid-dose [40 000 U/(kg?d)] urokinase group and high-dose [80 000 U/(kg?d)] urokinase group. Urokinase was administered by tail vein injection for 7 days. The affected vessels of the rats were harvested at the end of the experiment, and the alterations of endothelial cell number and collagen amount were measured via H&E staining and picrosirius red staining, respectively. Results: In stages I, II and III, the numbers of endothelial cells of the three urokinase treated groups were all significantly higher than that of model group (all P<0.05), but no statistical significances were noted between the urokinase groups (P>0.05). The percentages of the collagen-positive staining area of the three urokinase treated groups were all significantly lower than that of model group (all P<0.05), and this percentage was reduced with the increasing dose of urokinase. In stage IV, the numbers of endothelial cells of all of the three urokinase treated groups had no significant differences compared with model group (all P>0.05), while the percentages of the collagen-positive staining area of the three urokinase treated groups were all still significantly lower than that of model group (all P<0.05). Conclusion: Urokinase has significant protective effect on the endothelial cells and inhibitory effect on the collagen proliferation of the affected vessels within the first 14 days after thrombus formation. However, beyond 14 days after thrombus formation, urokinase has no effect on endothelial cells but still has inhibitory effect on collagen proliferation.