We demonstrate a novel magnetophoretic immunoassayof allergen-specific immunoglobulin E (IgE) based on themagnetophoretic deflection velocity of a microbead thatis proportional to the associated magnetic nanoparticlesunder enhanced magnetic field gradient in a microchannel. In this detection scheme, two types of house dustmites, Dermatophagoides farinae (D. farinae) andDermatophagoides pteronyssinus (D. pteronyssinus),were used as the model allergens. Polystyrene microbeadswere conjugated with each of the mite extracts followedby incubation with serum samples. The resulting mixturewas then reacted with magnetic nanoparticle-conjugatedanti-human IgE for detection of allergen-specific IgE byusing sandwich immuno-reactions. A ferromagnetic microstructure combined with a permanent magnet wasemployed to increase the magnetic field gradient (~104T/m) in a microfluidic device. The magnetophoreticvelocities of microbeads were measured in a microchannel under applied magnetic field, and the averaged velocity was well correlated with the concentration of allergen-specific IgE in serum. From the analysis of pooled seraobtained from 44 patients, the detection limits of theallergen-specific human IgEs for D. farinae andD. pteronyssinus were determined to be 565 (0.045IU/mL) and 268 fM (0.021 IU/mL), respectively. Thesevalues are 1 order of magnitude lower than those by aconventional CAP system. For evaluation of reproducibility and accuracy, unknown sera were subjected to ablind test by using the developed assay system, and theywere compared with the CAP system. As a result, coefficient of variance was less than 10%, and the developedmethod enabled a fast assay with a tiny amount of serum(~10 L).