The aim of this study was to investigate the distribution of aflatoxins and zearalenone levels in various corn-milling fractions. Corn kernels and six derived milling fractions (germ, bran, large and small grits, flour, and animal feed flour) were sampled in an industrial plant; both conventional and organic corns were sampled. To evaluate the effect of cooking, samples of polenta were prepared starting from naturally contaminated flour. Conventional and organic lots showed mycotoxin contamination. For both lots, germ, bran, and animal feed flour showed a marked concentration factor from 239 to 911% accounting for both the low yields of the derived products and the distribution of aflatoxins and zearalenone contamination in the outer parts of the kernels. Conversely, a reduction factor of at least four times from raw material to finished products was observed. Polenta samples were unaffected by the cooking process, with levels of contamination similar to those of starting flour.