Microwaves were used in the present work in order to destroy pure aflatoxins (model system), and yellow corn and peanuts containing aflatoxins (food system). Pure aflatoxins (B1, B2, G1 and G2) were individually coated on a silica gel and exposed to microwaves at various power settings and periods. The same technique was adopted for peanuts and yellow corn deliberately infected by Aspergillus flavus. The aflatoxins were extracted, fractionated by thin-layer chromatographic technique and quantitatively determined by spectrodensitometry. In all cases, the content of different aflatoxins in the deliberately infected yellow corn was in the decreasing order B1 = G1 > B2 > G2. Infected peanuts were characterized by the highest B1 level, being approximately 3, 2, and 4.4 times as great as that in B2, G1 and G2, respectively. The rate of aflatoxin destruction of model and food systems increased with the increase of microwave oven power setting (low, moderate and high) and exposure time to microwaves.