Using magnetic micro- and nanoparticles (beads) in microfluidic chips opens new perspectives for miniaturized applications in analytical sciences. Four important application areas of magnetic particles in microfluidic systems are discussed. The first one is that of manipulation of living cells. The latter can be labeled using magnetic beads that are specifically recognizing certain biomarkers on the cell surface. In this way, a well determined type of cells can be separated out of a complex matrix. Magnetic particles can also be used as substrates in a nucleic acid assay allowing specific detection and application in diagnosis. Immuno-assays represent another vast area of application for magnetic particles. The latter can either be used as mobile substrate in the assay, or the particle can play the role of magnetic detection label. Finally, a last field of application we discuss is the use of magnetic particles held in a microfluidic flow for catalytic applications.