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Abstract Background Studies have identified hemodynamic shear stress as an important determinant of endothelial function and atherosclerosis. In this study, we assess the influences of hemodynamic shear stress on carotid plaques. Methods Carotid stenosis phantoms with three severity (30, 50, 70%) were made from 10% polyvinyl alcohol (PVA) cryogel. The phantoms were placed in a pulsatile flow loop with the same systolic/diastolic phase (35/65) and inlet flow rate (16 L/h). Ultrasonic particle imaging velocimetry (Echo PIV) and computational fluid dynamics (CFD) were used to calculate the velocity profile and shear stress distribution in the carotid stenosis phantoms. Inlet/outlet boundary conditions used in CFD were extracted from Echo PIV experiments to make sure that the results were comparable. Results Echo PIV and CFD results showed that velocity was largest in 70% than those in 30 and 50% at peak systole. Echo PIV results indicated that shear stress was larger in the upper wall and the surface of plaque than in the center of vessel. CFD results demonstrated that wall shear stress in the upstream was larger than in downstream of plaque. There was no significant difference in average velocity obtained by CFD and Echo PIV in 30% (p = 0.25). Velocities measured by CFD in 50% (93.01 cm/s) and in 70% (115.07 cm/s) were larger than those by Echo PIV in 50% (60.26 ± 5.36 cm/s) and in 70% (89.11 ± 7.21 cm/s). Conclusions The results suggested that Echo PIV and CFD could obtain hemodynamic shear stress on carotid plaques. Higher WSS occurred in narrower arteries, and the shoulder of plaque bore higher WSS than in bottom part.