In this study, new magnetic manganese ferrite (MnFe 2O 4) nanoparticles with a size around 100 nanometer (nm) in diameter were used to improve the performance of an immunoassay for detection of influenza infection. A new microfluidic system was developed to implement the detection process. In order to apply these new nanoparticles for influenza detection, the design of the micromixer was modified to reduce the dead volume. Furthermore, the operating condition for the magnet was optimized such that magnetic MnFe 2O 4 nanoparticles can be collected in 120 seconds. The optical signals showed this nanoparticle-based immunoassay could successfully distinguish the virus sample from the negative control sample. This developed microfluidic system can automatically perform the entire process involved in the immunoassay, including virus purification and detection, and therefore may provide a promising platform for fast diagnosis of the infectious diseases.