In this study, we developed and analyzed different patient-specific 3D anatomical models of the left atrium including left atrial Appendage, in order to investigate the local hemodynamics. Particularly, we focused on the left atrial appendage and its impact on thrombus formation due to wall shear stress alterations. A 3D semi-automated reconstruction approach was carried out to segment and reconstruct the left atrium from CT scans. Six different patients were studied applying their patient-specific clinical data. Three different velocity profiles simulated for each patient case, representing one normal and two abnormal conditions. Simulations varied significantly according to different appendage morphologies. Our scope is to describe the hemodynamic behavior at the left atrium and the left atrial appendage according to different blood velocities based on their anatomic variety (chicken wing 0.14 m/s, windsock 0.10, cactus 0.08, and cauliflower 0.04). Wall shear stress results were demonstrated and correlated with the velocities and the thrombus formation inside the appendage cavity.