We describe a 63-year-old man in sinus rhythm (SR) with an ischaemic stroke involving basal ganglia region on the right side. The patient was known to be heterozygous for factor V Leiden (FVL) mutation. On diagnostic work-up, no arterial sources of embolism were found. Transoesophageal echocardiography evidenced a left atrial (LA) thrombosis without relevant cardiopathies. LA thrombosis is generally associated to atrial fibrillation, atrial enlargement, mitral valve stenosis and left ventricular dysfunction, whereas mitral regurgitation is considered protective. To our knowledge, this is the first report of cardioembolic stroke related to a LA thrombosis in a patient in SR without risk factors for thrombus formation except for FVL heterozygosity.