Blood is a shear-thinning non-Newtonian fluid in which the viscosity reduces with the shear rate. When simulating arterial flow, it is well established that the non-Newtonian nature is important in the smallest vessels; however, there is no consistent view as to whether it is required in larger arteries, such as the carotid. Here, we investigate the importance of incorporating a non-Newtonian model when applying a plaque deposition model which is based on near-wall local haemodynamic markers: the time-averaged near wall velocity and the ratio of the oscillatory shear index to the wall shear stress. In both cases the plaque deposition was similar between the Newtonian and non-Newtonian simulations, with the observed differences being no more significant than the differences between the selected markers. More significant differences were observed in the haemodynamic properties in the stenosed region, the most significant being that lower levels of near-wall reverse flow were observed for a non-Newtonian fluid.