BACKGROUND Anticoagulation remains a controversial issue among hyperthyroid patients with atrial fibrillation (AF). We aimed to evaluate the prevalence of the thrombogenic milieu (TM), detected using transesophageal echocardiography (TEE), among patients with AF related to hyperthyroidism, and to correlate these findings with the clinical embolic risk classification (CHA2DS2-VASc). METHODS CHA2DS2-VASc score, thyroid hormonal status, time since hyperthyroidism diagnosis, transthoracic echocardiography (TTE) and TEE were assessed in 47 consecutive patients aged between 18 and 65years with AF related to hyperthyroidism. The following TEE parameters defined TM: dense spontaneous echo contrast, thrombi, or left atrial appendage (LAA) blood flow velocities <0.20m/s. Non-classic TM was defined as non-dense SEC plus LAA flow velocity 0.20-0.40m/s. RESULTS Pulmonary hypertension was present in 39/47 (81.4%) and TM in 22/47 (46.8%) patients. Despite a low CHA2DS2-VASc score of 0/1, 10 of 19 (52.6%) patients had a TM, whereas 16 of 28 (57.1%) patients with score ≥2 had none. The probability of having a TM did not correlate with CHA2DS2-VASc scores. On regression binary analysis, hyperthyroidism diagnosed more than 12months previous was independently associated with non-classic TM (p=0.031). CONCLUSION Among patients younger than 65years of age with AF related to hyperthyroidism, pulmonary hypertension and TM on TEE were highly prevalent. There was no association between CHA2DS2-VASc with TEE markers of TM. Thyroid status, especially longer duration of hyperthyroidism might influence thrombogenic abnormalities. TEE adds useful information that may change antithrombotic therapy if otherwise guided solely by clinical risk classification.