Negative magnetophoresis of non-magnetic particles is the induced motion of non-magnetic particles suspended in magnetic media on the application of a magnetic field gradient. Negative magnetophoresis can be used to separate nanoparticles based on their size. An integrated finite-element model was developed using COMSOL to study the transport and separation of nonmagnetic particles in a negative magnetophoresis device. The model solves the magnetic field, fluid flow, and mass transfer equations in three dimensions. The model was used to successfully simulate an experimental separation device and was also used as a tool to develop modified designs that resulted in a substantial enhancement of the separation efficiency. In addition, the model successfully predicted the different phenomena that typically occur in a magnetophoretic device: trapping, focusing, and deflection. (c) 2015 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.