Systems and methods for the manipulation of particles within channels such as microfluidic channels are provided. In one set of embodiments, magnets are positioned around a channel. As a fluid containing magnetic and non-magnetic particles flows through the channel, the magnetic field created by the magnets can be used to transport the magnetic and/or non-magnetic particles to desired locations within the channel, which may useful in some cases for causing some separation of the particles. For example, the magnetic field may be used to transport magnetic or non-magnetic particles from a core fluid to a surrounding sheath fluid. In some cases, the magnetic field is used to transport non-magnetic particles to a small volume within the channel (e.g., a single-file row within the channel). The systems and methods described herein may find application in a variety of fields including, for example, continuous sorting of cells, removal of targeted cells from a stream of blood, or the arrangement of non-magnetic particles in channels for analysis.