Background: Atrial fibrillation (AF) confers a substantial increase in the risk of stroke. While the CHADS 2 score is considered a reliable predictor of stroke/thromboembolism risk in patients with AF, thromboembolism can occur even in AF patients with a low CHADS 2 score (CHADS 2 score = 0 or 1). We retrospectively assessed the relationships between left atrial appendage thrombus (LAAT) and patient characteristics, echocardiographic variables, and surrogate blood markers in patients with unanticoagulated AF, in order to determine whether thrombogenesis can be predicted in this patient population.Methods: The study group was comprised of 31 patients with unanticoagulated persistent non-valvular AF (NVAF) who underwent transthoracic echocardiography (TTE) and transesophageal echocardiography. Patients were divided into those with and without LAAT, and study variables were compared between the 2 groups.Results: LAAT was found in 14 patients. AF duration, left atrial diameter, left ventricular ejection fraction, left atrial appendage flow, β-thromboglobulin, platelet factor 4, prothrombin time, activated prothrombin time, fibrinogen, D-dimer, and antithrombin III levels did not differ between patients with and without LAAT. However, ANP and BNP levels were significantly higher in patients with LAAT (ANP ≥79 pg/ml, P = 0.03, BNP ≥120 pg/ml: P = 0.03). Moreover, patients with BNP ≥120 pg/ml exhibited an increased risk for LAAT (P = 0.03, odds ratio: 6.19), and patients with ANP ≥70 pg/ml in addition to BNP ≥120 pg/ml exhibited a further augmented risk for LAAT (P = 0.055, odds ratio: 8.75).Conclusions: In patients with unanticoagulated NVAF, a BNP level ≥120 pg/ml or an ANP level ≥70 pg/ml and BNP level ≥120 pg/ml could prove useful in predicting LAAT.