Background and objective: This study retrospectively investigated long term recurrence rate in stroke patients with atrial fibrillation (AF) who had left atrial thrombus (LAT). Methods: Participants compromised 359 consecutive stroke patients with AF less than 7 days after onset who had undergone transesophageal echocardiography. Patients were divided into LAT and non-LAT groups based on the presence or absence of LAT. Clinical background, neurological findings, imaging findings and stroke recurrence within 3 years of discharge were then compared between the two groups. Results: Fifty-nine patients were classified into the LAT group and 300 patients into the non-LAT group. Median age of the LAT and non-LAT groups was 78 and 76 years, respectively (p=0.57), and the LAT group had a higher proportion of females (53% vs. 39%, p=0.06) and hypertension (81% vs. 69%, p=0.06). CHADS2 score was higher in the LAT group than in the non-LAT group (median score: 3 vs. 2; p<0.01). Median National Institute of Health Stroke Scale score for the LAT and non-LAT groups was 7 vs. 4 (p=0.05). The proportion of patients with a maximum cerebral infarction diameter ≥3 cm was also greater in the LAT group (61%) compared to the non-LAT group (37%; p=0.02). The recurrence rate (RR) during hospital stay was 3.4% vs. 7.3%, respectively (p=0.40). However, cumulative RR for the 3-year period after discharge was significantly higher in the LAT group (25%) than in the non-LAT group (12%; HR, 2.61; p=0.03; Fig.1). Conclusion: Compared to patients without LAT, stroke patients with AF who previously had LAT are more likely to have increased recurrence in long term, but not in the short term.