Recent numerical studies of abdominal aortic aneurysm (AAA) suggest that intraluminal thrombus (ILT) may reduce the stress loading on the aneurysmal wall. Detailed fluid structure interaction (FSI) in the presence and absence of ILT may help predict AAA rupture risk better. Two patients, with varied AAA geometries and ILT structures, were studied and compared in detail. The patient specific 3D geometries were reconstructed from CT scans, and uncoupled FSI approach was applied. Complex flow trajectories within the AAA lumen indicated a viable mechanism for the formation and growth of the ILT. The resulting magnitude and location of the peak wall stresses was dependent on the shape of the AAA, and the ILT appeared to reduce wall stresses for both patients. Accordingly, the inclusion of ILT in stress analysis of AAA is of importance and would likely increase the accuracy of predicting AAA risk of rupture.