Background: Current international guidelines promote the use of stroke risk stratification tools to inform decision making about oral anticoagulant (OAC) use in atrial fibrillation (AF). Objectives: To examine (a) differences between CHADS2 and CHA2DS2VASc in classifying stroke risk in a primary care population of AF patients; (b) patterns of use of antithrombotics by stroke risk; and (c) patient and practice characteristics associated with use of oral anticoagulants in patients with AF. Methods: Cross-sectional multilevel modelling study of all patients with AF and without rheumatic heart disease or valve replacement (n = 21 564) from 315 Scottish General Practices. Results: (a) CHADS2 characterized 30.3% in the intermediate and 53.8% in the high-risk category, compared to CHA2DS2VASC only 9.7% intermediate and 85.1% high-risk. (b) Of included patients, 17.8% were currently not prescribed any antithrombotic and 43.3% were on OAC. OAC use was only weakly related to stroke risk. (c) Patients with paroxysmal AF and those with dementia and previous peptic ulcer (adjusted ORs 0.26, 0.25 and 0.79) were less likely to be prescribed OAC. OAC use varied over five-fold between practices after adjustment for patient case mix, with remote and non-training practices and those with high levels of high-risk prescribing being more likely to prescribe OAC. Conclusion: Evidence was found of both underuse and overuse of OAC in patients with AF. Promoting instruments for stroke risk assessment in AF is a plausible but untested strategy to improve decision making in AF, and its impact on OAC prescribing and patient outcomes should be evaluated in pragmatic trials.