BACKGROUND Although there has been growing concordance over what constitutes best practice in recent guidelines for treatment of atrial fibrillation (AF), notably regarding anticoagulant use, it remains unclear whether patients are being treated accordingly. AIMS The aims of this study were to explore the pattern of treatment pathways - i.e. how patients are treated over time - for patients with AF, and to test the hypothesis that comparative to patients in lower stroke-risk categories (as measured by CHADS(2) score), patients with higher CHADS(2) scores are less likely to discontinue anticoagulant therapy or, if not started on anticoagulant treatment, more likely to be transferred to anticoagulant therapy, in keeping with guideline recommendations. SETTING A total of 67,857 patients with a diagnosis of AF in practices registered with the General Practice Research Database. METHODS A series of possible treatment pathways were identified, and for each initial treatment, we estimated the probability of treatment change and the average time that a patient newly diagnosed with AF spent on a particular treatment, projected across 5 years and stratified by CHADS(2) score. RESULTS There was no relationship between CHADS(2) score and maintenance or discontinuation of particular approaches to antithrombotic treatment. While those beginning on antiplatelet therapy were more likely to change treatment than those on anticoagulants (approximately 60% vs. 50% within the first year), as much as one-third of treatment time of all those starting on a therapeutic approach involving anticoagulants featured no use of anticoagulants (either as monotherapy or in combination) over the 5-year period, and whether treatment was discontinued or maintained did not vary by CHADS(2) score. No difference was found in treatment pathways controlling for post-2002 diagnoses as against the whole sample. CONCLUSIONS Although there is more evidence of treatment maintenance than treatment change, especially in the first year after diagnosis, the amount of therapeutic change remains noteworthy and appears higher than in some previous studies. Prescription patterns for AF therapy suggest that too few high-risk patients are receiving best practice treatment, and particularly of concern is that some of these patients are being transferred away from best practice treatment over time.