Recent integrations of giant magnetoresistive sensor into laboratory-on-a-chip systems enable the direct detection of biological entities such as cells coated with magnetic particles on chip. However, before detection the different biological entities need to be separated. As a model system, we investigated the separation of two types of magnetic particles (4.5 and 2 mu m in diameter). The motion of the particles was studied when actuated using an alternating traveling magnetic field produced by four-phase conductors on chip. Different magnetic particles migrate with different speeds in the same traveling magnetic field. By carefully choosing the frequency of the magnetic field, different magnetic particles can be separated in a microfluidic system. (c) 2007 American Institute of Physics.