Thrombosis associated with atrial fibrillation (AF) is usually caused by a left atrial (LA) thrombus, but it is not always detected. The present study was based on the hypothesis that abnormalities in peripheral artery are responsible for the ischemic stroke associated with AF. Peripheral arterial coagulability was investigated in a rabbit experimental model in which AF was induced by high-frequency stimulation of the right atrium, creating stenosis of the carotid artery together with endothelial damage. The rabbits were classified into 4 groups: (i) sinus rhythm only (group 1), (ii) sinus rhythm after 6 h of pacing (group 2), (iii) short AF (continuous pacing for 5 min; group 3) and (iv) long AF (continuous pacing for 6 h: group 4). The carotid blood flow developed a typical pattern, called cyclic flow reductions (CFRs), the frequency of which (CFRF) was 18.59+/-2.85 in AF (group 3+4) compared with 14.46+/-2.1 in sinus rhythm (group 1+2) (p<0.0005). Among the groups with AF, correlation analysis showed an association between CFRF and pulse dispersion (p<0.02, r=0.58). This study suggests that the distinctive hemodynamic effects with AF, in particular pulse dispersion, substantively influence thrombus formation on injured vascular endothelium.