Arrhythmogenic right ventricular cardiomyopathy is a rare heart muscle disease characterized by right and often left ventricular myocardial atrophy and fibrofatty replacement. Heart failure, arrhythmias and sudden death are characteristic complications. We observed a female in whom arrhythmogenic right ventricular cardiomyopathy was diagnosed due to presyncopes and dyspnea on exertion. A left ventricular thrombus was found echocardiographically, which disappeared with oral anticoagulation. Subsequently, however, extensive thrombus formation in the dilated akinetic right ventricle occurred which was resistant to combined treatment with heparin and oral anticoagulation. Thrombophilia screening showed a mutant prothrombin 20210A allele which is an inherited coagulopathy associated with increased plasma levels of prothrombin and increased risks of mainly venous thrombosis. The patient developed endstage biventricular heart failure and underwent heart transplantation within 3 months after thrombus formation in the right ventricle was diagnosed. In the explanted heart, the thrombus in the right ventricle was impressively large and calcified. In patients with unusual thrombus formation in the heart, coagulopathy may be associated and should be excluded.