Atrial fibrillation (AF) renders individual patients at risk for development of an atrial thrombus. The aim of this study was to determine clinical and echocardiographic factors influencing the risk of left atrial thrombosis (LAT) in patients with persistent nonvalvular AF. Genetic variants encoding haemostatic factors have been also assessed for putative association with LAT. In the cross-sectional study, a total of 212 patients (132 males and 80 females) with nonvalvular persistent AF (duration range 48 h-90 days) have been selected. LAT was visualized by transesophageal echocardiography. The FGB G(-455)A, PAI-1 4G/5G, F5 C(-224)T, and F5 R506Q genetic markers were tested using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach. To reveal independent factors contributing to the thromboembolic risk in AF, a multivariate logistic model was applied. LA thrombi were found in 44 out of 212 subjects (21%). LAT was more frequently observed in patients at age >75 years (P < 0.001) and those who had reduced left ventricular ejection fraction <40% (LVEF; P < 0.001) and decreased left atrial appendage velocity <20 cm/s (LAAV; P < 0.001). Logistic regression analysis showed that advanced age (OR = 1.64 per decade P < 0.001), LVEF < 40% (OR = 2.12, P < 0.001), LAAV (OR = 1.56, P = 0.007), and TT genotype of F5 C(-224)T (OR = 2.42, P = 0.041) are associated with higher risk of LAT. Age >75 years, LVEF < 40%, LAAV < 20 cm/s, and Factor V C(-224)T variant independently contribute to the thromboembolic risk in AF.