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We use magnetic microbeads, which are magnetically self-assembled in chains in a microfluidic chip, as reaction substrates to implement two different sandwich immunoassay protocols for the detection of mouse monoclonal target antibodies. The magnetic chains form when the chip is placed in a magnetic field, and are geometrically trapped and accurately positioned in a microchannel with periodically enlarged cross-sections. In the first immunoassay protocol, capture and target antibodies are incubated off-chip, while exposure to the detection antibody is performed on-chip. In the second protocol, the complete immunoassay is fully executed on-chip. In the ‘off-chip incubation–on-chip detection’ protocol, antibodies can be detected down to a concentration of 50 ng/mL in a total assay time of 120 min, while consuming 1.5 mL of target antibody solution. Using the full on-chip protocol, our system is able to detect target antibodies in the range of a few ng/mL in 30 min, using only a few tens of nanoliters of target antibody solution and reagents. The ‘off-chip incubation–on-chip detection’ protocol is also applied for dosing antibodies obtained from the supernatant of a cell culture medium.