BACKGROUND: Despite the significant advances made in the field of computational fluid dynamics (CFD) to simulate the left atrium (LA) in atrial fibrillation (AF) conditions, the connection between atrial structure, flow dynamics, and blood stagnation in the left atrial appendage (LAA) remains unclear. Deepening our understanding of this relationship would have important clinical implications, as the thrombi formed within the LAA are one of the main causes of stroke. AIM: To highlight and better understand the fundamental role of the PV orientation in forming atrial flow patterns and systematically quantifying its effect on blood stasis within the LAA. METHODS: Two patients with opposite atrial flow patterns were selected for the study. The atria were segmented and subsequently morphed to modify the pulmonary vein (PV) orientations in a highly controlled manner. CFD analysis were performed using a kinematic model able to reproduce AF conditions. Results were projected into the universal left atrial appendage coordinate (ULAAC) system to enhance data visualization and comparison. RESULTS: The position of the main atrial vortex can be modified by controlled changes in the PV orientations, which to the best of our knowledge was not demonstrated before. This finding may have important clinical implications, as the behavior and position of the main atrial vortex is crucial to define the LA flow patterns and thus the LAA washing, making possible to assess the stroke risk for a particular patient.