In this paper, we investigated the effect of the fluid dynamical stress on islets during islet purification process. Firstly, we developed a fracture model of islets in a shear flow by the fracture test using a cylindrical viscometer. Secondary, we conducted the numerical calculation to estimate the fluid dynamical stress and strain energy during islet purification process. Finally we predicted the islet size reduction during islet purification using the fracture model and the numerical results. Comparing experimental data and numerical result in terms of the islet size reduction, it is confirmed that the fluid dynamical stress during the islet purification damages islets.