In order to determine the significance of microemboli in atrial fibrillation (AF), we used transcranial Doppler ultrasonography to study 27 AF patients with recent stroke, 27 AF patients without stroke and 19 sinus rhythm (SR) controls. Where possible, both middle cerebral arteries were monitored for 30 min. Microembolic signals were associated with clinical stroke (p = 0.05) but were no more prevalent in the AF group than in SR controls. In stroke patients, microembolic signals were independently related to recency of stroke onset (p = 0.01) and absence of anticoagulation (p = 0.05). There was no association between the hemisphere in which microembolic signals were detected and either stroke territory or carotid stenosis. Of the 27 asymptomatic AF patients, 20 were taking anticoagulants. There was no relation, however, between microembolic signals and anticoagulation status in this group, possibly due to small numbers. Embolus detection may be useful in confirming cardioembolic pathogenesis in acute stroke and therefore may influence choice of therapy.