This Ph.D. thesis presents theory, modeling, design, fabrication, experiments and results for microfluidic magnetic separators. A model for magnetic bead movement in a microfluidic channel is presented, and the limits of the model are discussed. The effective magnetic field gradient is defined, and it is argued that it is a good measure, when comparing the performance of magnetic bead separators. It is described how numeric modelling is used to aid the design of microfluidic magnetic separation systems. An example of a design optimization study is given. A robust fabrication scheme has been developed for fabrication of silicon based systems. This fabrication scheme is explained, and it is shown how, it is applied with variations for several designs of magnetic separators. An experimental setup for magnetic separation experiments has been developed. It has been coupled with an image analysis program to facilitate real-time monitoring of the experiments. The set-up and experimental protocol are described in detail. Results are presented for ’active’ magnetic bead separators, where on-chip microfabricated electromagnets supply the magnetic field and field gradients necessary for magnetic bead separation. It is shown conceptually how such a system can be applied for parallel biochemical processing in a microfluidic system. ’Passive’ magnetic separators are presented, where on-chip soft magnetic elements are magnetized by an external magnetic field and create strong magnetic fields and gradients inside a microfluidic channel. Systems with the elements placed beside the microfluidic channel is combined with hydrodynamic focusing to demonstrate a magnetic bead microarray inside a microfluidic channel. Systems where the on-chip magnetic material is placed underneath the microfluidic channel are also presented. One of these designs feature multiple magnetic length scales, and it is shown that this enhances bead capture ability. A ’hybrid’ magnetic separator design, where the magnetic field from on-chip current lines couples with an externally applied homogenous field to create strong fields and gradients is demonstrated. This gives extra magnetic bead manipulation possibilities compared to the passive designs. It is demonstrated how this can be used for magnetic bead microarrays. Finally, it is discussed, based on the research presented in this thesis, how to further develop magnetic separation systems in microfluidic systems, and recommendations are given for the choice of magnetic design based on the desired application.