Magnetic materials, such as ferrimagnetic and ferromagnetic nanoparticles and microparticles in the form of ferrofluids, can be advantageously used in micro-electro-mechanical systems (MEMS) and bioMEMS applications, as they possess several unique features that provide solutions for major microfluidic challenges. These materials come with a wide range of sizes, tunable magnetic properties and offer a stark magnetic contrast with respect to biological entities. Thus, these magnetic particles are readily and precisely maneuvered in microfluidic and biological environments. The surfaces of these particles offer a relatively large area that can be functionalized with diverse biochemical agents. The useful combination of selective biochemical functionalization and 'action-at-a-distance' that a magnetic field provides makes superparamagnetic particles useful for the application in micro-total analysis systems (micro-TAS). We provide insight into the microfluidic transport of magnetic particles and discuss various MEMS and bioMEMS applications.