BACKGROUND: Atrial fibrillation is a major cause of cardioembolic stroke. Since atrial and venous pressures are similar, genetic variants that promote venous thromboembolism may increase the risk of atrial thrombi and subsequent stroke in atrial fibrillation. METHODS: We conducted a nested case-control study of the association between the presence of factor V Leiden polymorphism and incident ischemic stroke within a prospective cohort of 13,559 adult patients with diagnosed nonvalvular atrial fibrillation between July 1, 1996 and December 31, 1997. Incident cases with ischemic strokes were identified through August 31, 1999 and matching stroke-free controls were enrolled. RESULTS: One hundred thirty-seven case patients with incident stroke and 214 controls were enrolled. Cases were older, more likely to be women, and more likely to have a prior stroke, heart failure, hypertension, diabetes, and coronary disease. The factor V Leiden polymorphism was present in 5.8% of cases and 3.7% of controls (P = 0.36). Among non-anticoagulated patients, 7/96 (7.3%) case patients and 3/81 (3.6%) control subjects were heterozygous for factor V Leiden (Odds Ratio 2.1 [95% CI: 0.5-8.4]). Adjustment for known stroke risk factors did not significantly change the observed association in non-anticoagulated patients (adjusted OR 1.9 [0.5-8.0]). CONCLUSIONS: Within a large nested case-control sample of patients with atrial fibrillation, factor V Leiden was not significantly associated with risk of stroke. However, given the suggestive nature of our findings, further study in even larger numbers of patients is needed to clarify the impact of factor V Leiden on stroke risk in atrial fibrillation.