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Background: Atrial fibrillation (AF) is a major risk factor for ischemic stroke, myocardial infarction, congestive heart failure and long term mortality. Atherosclerosis disease may co-exist in ischemic stroke patients with AF. Until now, there is limited information on the impact of concomitant carotid atherosclerosis on long-term outcomes in ischemic stroke patients with AF. Thus, we investigated where there are differences in long-term mortality among ischemic stroke patients with AF.Methods: Total 343 ischemic stroke patients with AF who underwent carotid ultrasonography between January 2007 and December 2013 were enrolled in this study. Total number of carotid artery plaque and maximal thickness among carotid plaques were assessed using B-mode ultrasound. For measuring carotid plaque burden, we made the carotid plaque burden score, which was calculated by multiplying the total number of carotid artery plaques and the maximal thickness. The association between carotid plaque burden score and long-term mortality was investigated using Cox hazard model.Results: After a mean follow up period of 3.2 years, total 69 patients (20.1%) dead. Mean carotid plaque burden score was 11.76 ± 15.32 (mean ± Standard Deviation). In univariate analysis, age ((HR, 1.07; 95% Confidence Interval [CI], 1.01-1.10, P<0.001), initial National Institute of Health Stroke Scale (HR, 1.09; 95% CI, 1.06-1.13, P<0.001), and plaque score (HR, 1.02; 95% CI, 1.01-1.03, P<0.001) were significantly associated with all-cause mortality in ischemic stroke patients with AF. In multivariate analysis, after adjusting conventional cardiovascular risk factor, carotid artery plaque burden score was independently associated with all-cause mortality in ischemic stroke patients with AF (HR, 1.03;95% CI, 1.01-1.04, P<0.001).Conclusion: Carotid plaque burden is an independent predictor of all-cause mortality in ischemic stroke patient with AF. Intervention of atherosclerosis may help to improve long term outcome in ischemic stroke patients with AF.