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Mold contamination in agricultural commodities including grains, grain-based foods, fruits, and vegetables was investigated by two analytical methods. One method employed a mixed monoclonal antibody sandwich ELISA for detection of Aspergillus, Penicillium and Fusarium genera-specific antigens. The detection limit of ELISA for these antigens was 100 ng/g. The other protocol was HPLC-based detection of ergosterol, the predominant sterol in most molds. Recoveries of ergosterol from grains and grain-based foods at spiking levels of 50–1000 ng g−1 ranged between 82 and 86%. The detection limit of the HPLC method for ergosterol was 40 ng g−1. Ninety-two samples (59%) and 116 (75%) among 155 samples tested positive with antigens and ergosterol by the ELISA and the HPLC method, respectively. The cause of conflicting data between both detection methods found in nine dried persimmon samples were solved by using the conventional direct plating method that showed the prevalence of other genera with rarity of Aspergillus, Penicillium and Fusarium. The sandwich ELISA method offers a rapid assay for selectively tracing the potential mycotoxigenic mold, and also is a preliminary screening method for mycotoxin analysis.