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In this study, we developed a novel tool for purifying two mycotoxins, aflatoxin B1 (AFB1) and zearalenone (ZEN), in feed. This system utilized monoclonal antibodies (mAbs) against AFB1 and ZEN, and magnetic nanoparticles (MNPs). Among ten MNPs with different diameters and functional groups, a 100-nm diameter MNP (fMA) conjugated to an amine group (-NH2) was found to be optimum for coupling with mAbs. The optimal mAb concentrations for coupling to the fMA along with mycotoxin purification capacities of the fMA-mAb conjugates (fMA-AFB1 and fMA-ZEN) were determined. A comparison of mean recovery rates (from corn and product X feed) between the fMA-mAb conjugates and immunoaffinity columns (IAC-AFB1 and IAC-ZEN) showed that the rate for fMA-AFB1 (90∼92% and 81∼88%) was higher (p > 0.05) than that of IAC-AFB1 (81∼84% and 72∼78%) for AFB1 (5, 10, 15 ng/mL), and the rate for fMA-ZEN (99∼100% and 92∼94%) was significantly higher (p < 0.01) than that of IAC-ZEN (86∼88% and 81∼88%) for ZEN (10,25, 50 ng/mL) except at a concentration of 10 ng/mL, demonstrating the remarkable purification efficiency of the novel fMA-mAb method. Additionally, mycotoxin purification was much faster using our novel method (approx. 5 min) than the IAC-based technique (> 30 min). This study suggests that the novel purification system we developed would be a useful tool for monitoring and regulating mycotoxin contaminatio in feed, and replace IAC methods.