Objective: We have previously shown that atherosclerotic apolipoprotein E-deficient (apoE^-/-) x LDL receptor-deficient (LDLR^-/-) mice develop myocardial infarction when exposed to hypoxic stress. This study was performed to assess the role of thrombin and thrombosis in this process. Methods: ApoE^-/- x LDLR^-/- mice were fed a cholesterol-rich diet for 8 months and then subjected to hypoxic stress during isoflurane anesthesia. One group received a bolus dose (5.6 µmol/kg) of the thrombin inhibitor melagatran and controls received PBS 10 min before the hypoxic stress. The mice were exposed to 10 min of hypoxia followed by normoxia. 10 min after the stress, Alzet pumps delivering melagatran (20 nmol/kg/min) or PBS were implanted and the mice were allowed recovering for 48 hrs. The cardiac response was analyzed by histology, immunohistochemistry and serum troponin T assay. Results: All animals showed reversible ECG changes as sign of ischemia during hypoxic stress and 50% developed infarctions afterwards as judged by troponin T levels. The group receiving thrombin inhibitor had significantly lower troponin T and smaller myocardial infarctions than the PBS treated group. These data show that thrombin generation is an important pathogenetic factor and suggest that coronary thrombosis is involved in myocardial infarction in atherosclerotic mice. Conclusion: Exposure of atherosclerotic mice to hypoxia leads to myocardial infarction through a two-phase pathway, in which acute transient ischemia is followed by thrombin dependent irreversible myocardial ischemia and myocardial cell death.