The CHA(2)DS(2)-VASc score was developed to improve stroke risk stratification in atrial fibrillation (AF) patients. We sought to analyze the distribution and prognostic value of the CHA(2)DS(2)-VASc score in a cohort of ischemic stroke patients with AF. In total, 439 consecutive stroke patients with AF were studied. The CHA(2)DS(2)-VASc score was calculated according to clinical status before stroke onset. Poor outcome was defined as a modified Rankin score of 3 to 6 at 3 months. Association between CHA(2)DS(2)-VASc score and poor outcome was analyzed using logistic regression analysis. In 95.6% of patients, CHA(2)DS(2)-VASc was >1 and only 41.8% of those with previously diagnosed AF were using oral anticoagulation at the time of the stroke. Poor outcome was found in 53.1% of the patients. In univariate analysis age, female sex, current smoking, previous stroke, CHA(2)DS(2)-VASc score, and stroke severity were associated with outcome. In multivariate analysis, CHA(2)DS(2)-VASc score was independently associated with poor outcome [OR 1.36 (95% CI: 1.14-1.62), P = 0.001] as well as NIHSS [OR 1.22 (95% CI: 1.17-1.26), P < 0.001]. After removing stroke severity, therapeutic anticoagulation was also associated with stroke prognosis [OR 0.45 (95% CI: 0.23-0.86), P = 0.016]. Most patients with ischemic stroke and AF have a high CHA(2)DS(2)-VASc score. Independent of stroke severity, CHA(2)DS(2)-VASc score is associated with 3-month outcome. Despite all the available information and guidelines, our AF patients are clearly undertreated.