Previous research has observed concentration polarization in LDL and HDL in the arterial system. However, there is no report that links this concentration polarization to the development of vascular atherosclerosis (AS). Therefore, the purpose of this study is to establish the relationship between concentration difference of LDL and HDL and shear stress using a carotid bifurcation vascular model. PTFE was employed to create the carotid bifurcation model. Endothelial cells were coated on the inner wall of the graft. In a recirculation system, HDL and LDL concentration were measured under two different ICA flow velocities at 5 different locations within our model. We report the following: (1) LDL and HDL concentration difference was observed in both high flow and low flow environments; (2) the degree of LDL and HDL concentration polarization varied depending of high flow and low flow environment; (3) absolute values of concentration difference between LDL and HDL at the inner wall surface decreased with the increase in shear stress when shear stress was more than 1.5 Pa. This variation trend would be more pronounced if shear stress were less than 0.5 Pa. Our study suggests that under the action of shear stress, concentration differences of LDL or HDL create a disturbance in the balance of atherogenic factors and anti-As factors, resulting in the occurrence of AS.