Although drug-eluting stents (DESs) can decrease the risk of restenosis, this benefit is tempered by a possible increased risk of in-stent thrombosis. We assessed the effects of rapamycin on human umbilical vein endothelial cells (HUVECs) to identify the alterations in gene expression associated with thrombosis. Expression of tissue plasminogen activator (t-PA) and plasminogen activator inhibitor 1 (PAI-1) was assessed in HUVECs treated with rapamycin (final concentrations: 1, 10, 100, and 1000 ng/mL) for 24 and 48 hours. Incubation of HUVECs with rapamycin strongly reduced the expression of t-PA in a concentration-dependant manner (P < .05 to < .01). However, the expression of PAI-1 was induced by rapamycin (P < .05 to < .01). The increase in PAI-1 induction was up to 3.3-fold. In conclusion, rapamycin inhibited t-PA and induced PAI-1 expression in HUVECs. This effect may contribute to in-stent thrombosis associated with DESs.