Background: Patients with acute cardio-embolic stroke from atrial fibrillation (AF) are at risk for recurrence with up to 50% of recurrent stroke occurring within two weeks of the index event. Anti-coagulation with heparinoids within 48 hours of stroke has been shown to increase risk of symptomatic intracranial hemorrhage (ICH) with no clear benefit on early stroke recurrence. Methods: This study was a retrospective chart review of consecutive patients who were admitted to the stroke service at the Foothills Medical Centre between 2009 and 2011. All patients with an acute stroke with a cardio-embolic etiology and a diagnosis of atrial fibrillation were reviewed. We hypothesized that anti-coagulation within two weeks of stroke, appropriately begun because of a diagnosis of AF, decreased rates of recurrent stroke without causing an increase in rates of symptomatic ICH. Results: Between 2009-2011, 324 patients were identified with cardio-embolic stroke secondary to AF. Within two weeks of stroke onset 61.4% (199/324) of patients were therapeutic on anti-coagulation. Patients who were anti-coagulated had a smaller median index stroke volume (3.2 ml vs 18.4 ml). Three (0.9%) patients suffered a clinically significant ICH. Recurrent stroke occurred in 11 patients (3.4%) within the two-week period. Therapeutic anti-coagulation within two weeks of initial stroke was associated with a decreased risk of recurrent stroke (RR 0.1, 95% CI 0.03-0.64). Conclusions: Anti-coagulation within two weeks of acute stroke in patients with AF appears to be safe among patients with smaller infarcts and prevents early recurrent infarction.