Thrombosis in a native aortic valve is a rare complication which may lead to systemic embolization. A few cases of aortic thrombosis in previously abnormal valves have been described. In this report, we describe a 42-year-old male who suffered two acute ischaemic attacks, one in the upper right limb and another in the cerebral territory supplied by the left sylvian artery, from a thrombus that developed in a bicuspid and stenotic aortic valve. The diagnosis was made with transthoracic and transoesophageal echocardiography, and the patient subsequently underwent surgery. In cases of bicuspid aortic valves, we should think of thrombosis as a possible complication with its resulting risk of embolism, and assess such patients with transthoracic and transoesophageal echocardiography, thus enabling their early detection and treatment.