In the Quadrupole Magnetic Sorter (QMS) magnetic particles enter a vertical flow annulus and are separated from non-magnetic particles by radial deflection into an outer annulus where the purified magnetic particles are collected via a flow splitter. The purity of magnetically isolated particles in QMS is affected by the migration of nonmagnetic particles across transport lamina in the annular flow channel. Computational Fluid Dynamics (CFD) simulations were used to predict the flow patterns, pressure drop and nonspecific crossover in QMS flow channel for the isolation of pancreatic islets of Langerhans. Simulation results were compared with the experimental results to validate the CFD model. Results of the simulations were used to show that one design gives up to 10% less nonspecific crossover than another and this model can be used to optimise the flow channel design to achieve maximum purity of magnetic particles.