CONTEXT: Plasma brain natriuretic peptide (BNP) levels are elevated in patients with acute ischemic stroke, particularly when accompanied by atrial fibrillation (AF). Plasma BNP might be a useful marker of vulnerability to thromboembolism in non-valvular AF patients. AIM: The aim of the present study was to assess whether the BNP level can serve as a biomarker of the left atrial (LA) thrombus in AF patients with acute ischemic stroke. SETTINGS AND DESIGN: This was a multicenter prospective cohort study. PATIENTS AND METHODS: Thirty AF patients with acute ischemic stroke were included in the study. Their transesophageal echocardiography (TEE) and BNP were assessed. RESULTS: There was a positive significant relation between serum BNP levels and LA thrombus detection by TEE. BNP with a cutoff value >498 pg/l can be used as a diagnostic biomarker for the presence of the LA thrombus. A significant positive correlation existed between serum BNP and LA diameter. Furthermore, a statistically significant positive correlation between serum BNP and AF rate and duration was found in all patients. In addition, a statistically significant inverse correlation was detected between serum BNP and direct bilirubin, international normalized ratio, and albumin. A statistically significant positive correlation existed between serum BNP and prothrombin concentration. CONCLUSION: BNP can be a good diagnostic biomarker for the detection of the LA thrombus in chronic AF patients with acute ischemic stroke.