Atrial fibrillation (AF) diminishes left atrial (LA) mechanical function and impairs blood flow. The latter can lead to blood stasis and increased risk of thrombus formation and stroke. We investigate this risk by studying the effects of LA flow in sinus rhythm (SR) and AF on blood coagulation dynamics.Patient-specific computational fluid dynamics (CFD) simulations were coupled with the reaction-diffusionconvection equation for thrombin. Patient LA wall motions driving the flow were reconstructed from Cine MRI data during SR and AF. 15 cardiac cycles were simulated for each patient to evaluate the likelihood of thrombus formation in the critical left atrial appendage (LAA) and right inferior pulmonary vein (RIPV) regions.The simulations showed that mean blood flow velocity in the LA cavity was substantially decreased (47%) during AF compared to SR. Specifically in LAA, mean flow velocities decreased from 0.06m/s in SR to 0.035m/s in AF, leading to enhanced thrombin generation. In the RIPV, higher mean flow velocities (0.16m/s) enabled thrombin washout through the mitral valve irrespective of SR or AF.This study proposes a novel modelling approach for quantifying the likelihood of AF-related thrombogenesis within LA and demonstrates increased risk of thrombus formation in the LAA when compared with the RIPV.