The management of anticoagulant therapy in patients with atrial fibrillation undergoing electrical cardioversion remains controversial, largely because of inadequate studies demonstrating risk or benefit, a relatively inconvenient anticoagulation management strategy and the increasing use of transesophageal echocardiography. Recent investigations into the potential mechanisms involved in the development of thrombus and systemic embolism in patients undergoing electrical cardioversion of atrial fibrillation may provide insight into underlying predisposing factors, with subsequent modification of management strategies. Conventional wisdom suggests that preexisting thrombus is responsible for thromboembolic events after cardioversion. However, development of a thrombogenic milieu after cardioversion, particularly in the left atrial appendage, may also be an important predisposing factor. To protect against both potential mechanisms of embolization, these data support therapeutic anticoagulation for all patients with atrial fibrillation of > 2 days in duration from the time of, as well as after cardioversion for a total of 4 weeks, undergoing cardioversion, even in the absence of thrombus on echocardiography. Therefore, the role of transesophageal echocardiography in this setting should be to enable early cardioversion if atrial thrombus is excluded and to identify high risk patients with atrial thrombi so as to postpone cardioversion and avoid the risk of embolization. Ultimately, however, a controlled, randomized and prospective clinical trial will be required to compare conventional management with a transesophageal echocardiography-guided strategy.