Native aortic valve thrombosis is an uncommon event with heart valve disease, during cardiac catheterization, bacterial endocarditis, or a hypercoagulative state as in antiphospholipid antibody syndrome. We report a case of thrombus formation on a native aortic valve, which was found by the transesophageal echocardiography during thrombectomy of the lower limb. We supposed that the atheromatous plaque of aortic valve was related to thrombus formation.