We present techniques and methodologies for the manipulation of magnetic micro- and nanoparticles ('beads') in microfluidic systems. We first introduce the most important forces that act on magnetic particles in a microfluidic system. Starting with the magnetic force that is responsible for the primary actuation of the magnetic particles, we discuss the viscous drag force induced when the particles are moving with a speed different from the liquid in the microfluidic channel. These forces can be combined in time and space to realize the basic manipulation steps of magnetic beads in a microfluidic system: retention, separation, mixing and transport. We also discuss the use of beads as magnetic detection labels or as magnetic force mediators inside droplets.