Cardioversion in patients with atrial fibrillation is associated with an increased risk of embolic stroke. Screening for atrial thrombi with transesophageal echocardiography (TEE) before cardioversion should, in many patients, permit safe cardioversion to be done earlier than it would be possible with a prolonged conventional anticoagulation therapy. The aim of the study was to compare the feasibility and safety of transesophageal echocardiography-guided early cardioversion with those of conventional management of cardioversion in patients with atrial fibrilation. The study involved 95 patients with persistent atrial fibrillation lasting longer than two days and having cardioversion. Forty patients underwent transesophageal echocardiography before cardioversion, with a short-term anticoagulation therapy. Cardioversion was conventionally guided in 55 patients (a long-term anticoagulation therapy and only transthoracal echocardiography). Atrial thrombi were detected in 20% of TEE group patients and led to the postponement of cardioversion. No embolization was recorded with this strategy. Embolization occurred in 6% of patients in the group receiving the conventional therapy. The cardioversion treatment was shorter in the TEE group (p < 0.001). Cardioversion was successful in 92% patients of the TEE group, and 78% patients of the conventional group. These results suggest that TEE-guided cardioversion is feasible and safe. The use of TEE may allow cardioversion to be done earlier, may decrease the risk of embolism associated with cardioversion.