A novel method of controlled transport of proteins immobilized on micrometre-sized magnetic beads in a lab-on-a-chip environment is presented. Bead motion is controlled by lithographically made magnetic elements forming transportation lines in combination with an applied in-plane rotating magnetic field. In this way, transport of attomole amounts of proteins is controlled with micrometre precision. Also, the activity of proteins immobilized on the beads is demonstrated by injecting antibodies into the system. A critical step in developing the method was to reduce sticking forces between beads and substrate during transportation of proteins. Charge interaction was found to be of minor importance compared to hydrophobic forces. To achieve a reliable transport of biologically active proteins, both substrate and beads were coated with polyethylene glycol (PEG) and the protein covered beads were suspended in buffer with surfactants. The described system fulfils all the important unit operations of a microfluidic platform and, as a further advantage, presents less need for microchannels and electric wiring.