AbstractBackground:The goal of our bioassay technique is to demonstrate high throughput, highly parallel, and high sensitivity quantitative molecular analysis that will expand current biomedical research capabilities. To this end, we have built and characterized a magnetophoresis instrument using a flow chamber in a magnetic field gradient to sort magnetic microparticles by their magnetic moment for eventual use as biological labels.Methods:The flow chamber consists of a sample inlet, differential sheath streams, and eight outlets for collecting the microparticles after they have traversed the chamber. Magnetic microparticles are injected into the flow chamber that is positioned in a linear magnetic field gradient. The trajectory for each microparticle is determined by its total magnetic moment and size. The resulting populations of monodispersed magnetic microparticles in the different outlet bins are sorted by their magnetic moment; with the highest magnetic moments being deflected the furthest.Results:We have characterized the system for sorting both superparamagnetic and ferromagnetic microparticles with approximate diameters of 8 μm and 4.0–4.9 μm, respectively. To characterize the instrument, we used microparticles with a known size distribution and varied the transit time through the chamber. This is equivalent to varying the magnetic moment, while allowing us to hold the particle properties constant from run‐to‐run. We demonstrated the ability to reproducibly change the distribution of the particles in the collection bins by varying transit time in good agreement with theory. We identified hydrodynamic instabilities responsible for causing dispersion in the flow. Improvements to the flow chamber hydrodynamics such as reducing the aspect ratio between the sample inlet and the chamber depth and stabilizing the sheath flow resulted in narrow sorting distributions. We measured a sorting reproducibility (percentage of particles returning to their original bin upon resorting individual populations) of 84–89%.Conclusions:We have developed a simple magnetophoresis system for reproducibly sorting magnetic microparticles. This technique will permit the use of microparticles with a wide range of magnetic moments to create a wide range of magnetic labels. Careful consideration of system design and operational parameters enables reliable and reproducible sorting of microparticles with varying size and magnetic content. © 2006 International Society for Analytical Cytology