Complexity of the spatial configuration of an aortic implant with bifurcation in the distal part is related to changes in blood hemodynamic in the area of bifurcation which may disturb blood flow and lead to thrombus formation. This study was designed to characterize parameters which define spatial configuration of an aortic implant for which the risk of thrombus formation is the smallest. We used AngioCT data from 74 patients, aged 55 ±10 years, after endovascular procedure to prepare 3D geometries of stent-grafts. Computational Fluid Dynamics (CFD) simulations were used to reconstruct blood hemodynamic and simulate thrombus formation. Next, geometric parameters of stent-grafts included the ratio of volume of upper part to the bifurcations, the relation of inlet and outlet diameters of a stent-graft and deformations in the iliac part of the stent-graft were analyzed. We also analyzed tortuosities (spiral twisting of the flow around the flow direction) and bends (the largest angulation in distal part of a stent-graft). The CFD results were confronted with AngioCT data to verify if computer generated thrombus appeared in particular patient. Additionally, geometric parameters of analyzed stent-grafts were used to propose a mathematical tool for prediction of thrombus appearance. The results showed that tortuosities and bends of a stent-graft had the highest impact on thrombus formation. Formation of thrombi was observed in 22% to 31% of cases (at blood hematocrit Hct = 40%) even for small values of tortuosities and bends indicating that these parameters are dominant in determining blood clotting. Our calculated results overlapped with clinical data in 80% to 91%. Therefore, we conclude that tortuosities and bends have high impact on thrombus formation and should be under special attention during stent-graft recommendation and patients' follow-ups.