The separation of magnetic microparticles suspended in a finite volume of fluid-a process that involves the interaction of magnetic and hydrodynamic forces-was modeled in two steps with commercially available finite-element analysis software. The first step was the steady-state modeling of the magnetic force on a magnetic microparticle throughout the region of the fluid container. In the second step, a fluid dynamics software package was used to predict the transient fluid velocity and particle concentration distributions during the separation process. This modeling method revealed that fluid motion and consequent particle convection are the major mechanism of particle motion during separation. The fluid motion patterns, moreover, undergo significant changes during the course of the separation. These patterns agree qualitatively with experimental observations of fluid flow during magnetic separation. This modeling technique allows analysis of the effects of varying magnet configuration, particle characteristics, and container geometry on the magnetic separation process.