Prevention of arterial thrombotic diseases has high priority in developed countries. As inappropriate diet is known to enhance the risk for acute thrombotic events, a regular diet with experimentally proven antithrombotic effect might be a beneficial way of prevention. The present study is part of a series of investigations testing fruits and vegetables for antithrombotic activity. The Global Thrombosis Test was used to screen sixteen different apple varieties for antiplatelet and thrombolytic activities. The in vitro effective varieties were further investigated using the laser-induced thrombosis model in mice. In order to investigate the mechanism, hemostatometry and flow-mediated vasodilation test (FMV) were performed. Apple varieties were grouped into subclasses according to their antithrombotic activity. AP-2, AP-13, AP-14 and AP-15 showed significant antithrombotic effect both in vitro and in vivo. AP-8 was antithrombotic in vitro but could not determine in vivo because of the shortage of the sample. The antithrombotic effect was mainly due to activation of endogenous thrombolytic mechanism. The mechanism of such enhanced thrombolysis was investigated using a synthetic inhibitor highly specific to plasmin, polyclonal IgG to t-PA and u-PA, and testing the antithrombotic effect in t-PA knockout mice. Antithrombotic activity was prevented by the synthetic plasmin inhibitor and IgG against t-PA but not against u-PA. There was no antithrombotic activity in t-PA knockout mice. Intake of antithrombotic apple filtrate did not affect FMV and platelet reactivity. The antithrombotic effect was heat stable at 100 °C for 10 min. These results suggest that the mechanism of antithrombotic activity involves an increased t-PA release from the vascular endothelium and an inhibition of plasminogen activator inhibitor (PAI-1) release from activated platelets. The present findings justify including antithrombotic apple varieties in an antithrombotic diet.