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Magnetic particles have become a promising tool for nearly all major lab-on-a-chip (LOC) applications, from sample capturing, purification, enrichment, transport to detection. For biological applications, the use of magnetic particles is especially well established for immunomagnetic separation. There is a great amount of interest in the automation of cell sorting and counting with magnetic particles in LOC platforms. So far, despite great efforts, only few fully functional LOC devices have been described and further integration is necessary. In this review, we will describe the physics of magnetic cell sorting and counting in LOC formats with a special focus on recent progress in the field.