A device for treating an analyte using magnetic beads is provided wherein the surfaces of the magnetic beads are effectively available as a whole. The device comprises a housing having a channel therein, through which channel the analyte is moved; a pair of electromagnets which are oppositely arranged in such a manner that the channel is interposed therebetween; a moving means for moving the pair of electromagnets along the channel while the electromagnets are facing the channel; and a controlling means for controlling magnetic forces generated by the electromagnets. The device is characterized in that the magnetic forces of the electromagnets are alternately generated with time. This will cause the magnetic beads to collide successively with the inner surface of the channel, which in turn gives a more efficient dispersion of the magnetic beads even if they are clustered or agglutinated to each other.