Superior mesenteric artery embolisation is the most common cause of acute mesenteric ischaemia. Superior mesenteric artery embolisation can be caused by various cardiac diseases (myocardial ischaemia or infarction, atrial tachyarrhythmias, endocarditis, cardiomyopathies, ventricular aneurysms and valvular disorders), arterial aneurysms, ulcerated atherosclerotic plaques of the major arteries and others. A case of 65-year-old, previously healthy man with superior mesenteric artery embolism, who was found to also have mural aortic thrombi, is presented. The patient underwent an emergency procedure; small intestine and cecum were resected and jejuno-ascendo anastomosis was performed. The patient was put on lifelong anticoagulation therapy. Neither cardiac diseases nor arterial aneurysms were detected. There were no signs of underlying atherosclerosis. Work-up for antiphospholipid antibodies and rheumatic diseases was negative. Tumour markers were within normal levels and blood cultures were negative. This case represents the challenges in recognising an underlying cause of acute mesenteric embolism and highlights the importance of multidisciplinary diagnostic and treatment approach.