Wheat, like other plants, can be attacked by a range of fungal pathogens which cause disease. Some of these also produce mycotoxins which are poisonous chemical compounds. There are five groups of mycotoxins found in food but only a few are regularly encountered on wheat. Mycotoxins have great significance in the health of both humans and livestock.

The mycotoxins of greatest significance on wheat are those produced by the head blight fungi on the growing crop (Fusarium graminearum and Fusarium culmorum). These are deoxynivalenol (DON) and zearalenone (ZON). Another mycotoxin, ochratoxin A (OTA) is produced by the fungi Penicillium and Aspergillus which grow on mouldy grain in stores.

The whole cereals supply chain is vigilant in checking for the presence of these mycotoxins, for which maximum levels are set to ensure that they do not enter the human food chain. Industry monitoring programmes exist for them.