It is rare to find aortic root thrombi in the absence of aortic root aneurysm or extensive aortic atherosclerosis. Up to this date, only a few cases have been reported. The etiology has been mainly attributed to hypercoagulable disorders. Herein, we present a case of a large thrombus obliterating the aortic root in a patient presenting with acute abdominal pain and noted to have showers of emboli to the kidneys. Hypercoagulable workup failed to reveal any congenital or acquired clotting disorder. The thrombus was thought to have developed spontaneously, and was removed surgically. Two months later, however, she had an arterial clot in the left popliteal artery that was removed surgically. The patient was seen for follow-up three and six months later and was stable with no complaints. This case highlights the importance of considering the ascending aorta as a source in cases of systemic embolization. In addition, the different diagnostic options, management protocols, and potential complications are discussed.