Mycotoxins are secondary metabolites with potential dangers for animal and human health. In particular, maize (Zea mays L.) infection caused by Fusarium and the consequent fumonisin contamination is widespread in several countries such as Italy. We developed six maize populations differing in their constitution of regulatory genes able to accumulate respectively anthocyanins in the aleurone layer (r1 gene), pericarp (b1 and pl1 genes) and phlobaphene in the pericarp (p1 gene). These coloured populations, with the related control colourless populations were analysed for mycotoxin content in the kernels during three field seasons with the aim of understanding if there were any correlations with their ability to accumulate flavonoids in kernel tissues. Our results indicate that accumulation of flavonoid pigments in the seeds, in particular phlobaphenes, is able to reduce the level of fumonisin B1. This finding could be used to minimize kernel mycotoxin contamination in this crop, in particular, the development of sweet, pop and polenta coloured corn varieties will help the farmer to keep the level of fumonisin under the threshold of contamination established for human corn consumption.