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In the present study, a magnetic droplet-handling system using magnetic beads as a reaction carrier have been developed and applied for biochemical analysis system. The droplet-handling mechanism is a novel type of handling solution that does not need mechanical devices such as pumps and valves. Results show that enzymatic reaction can be performed in the proposed droplet-handling system without losing their enzymatic activity. The developed droplet-handling system enables separation and fusion of droplets containing magnetic beads only by manipulation of magnet. Concentration and rinsing of target biomolecules is also possible in this mechanisms. The developed droplet-handling system might be applicable for on site immunoassays and gene analyses.