It is well known that the altered blood flow is related to vascular diseases, including atherosclerosis, restenosis, and arteriosclerosis, which preferentially located at areas with the disturbed blood flow, suggesting that altered biomechanical stress may exert their effect on the vascular disease. Recent evidence indicated the presence of abundant stem/progenitor cells in the vessel wall, in which laminar shear stress can stimulate these cells to differentiate towards endothelial lineage, while cyclic strain results in smooth muscle differentiation. In line with this, it was evidenced that altered biomechanical stress in stented vessels may lead to 'wrong' direction of vascular stem cell differentiation resulting in restenosis. However, the underlying mechanisms are not well understood. In this article, we will give an overview of the effect of the local flow pattern on stem/progenitor cell differentiation and the possible mechanism on how the blood flow influences stem cell behaviours in the development of vascular diseases.