Mycotoxins can form in oats in the field or following harvesting. In order to prevent the post-harvest formation of mycotoxins, the unprocessed oats are dried following arrival at the feed mill to prevent the formation of storage mycotoxins such as those produced by
Penicillium species. Teagasc report that the moisture content of oats should be between 14.5 and 15% to prevent fungal growth during long term storage. Oats are normally harvested from mid-July to mid-September with the majority completed in August, but it depends on weather conditions. Oats are stored following drying in sheds or in silos until they are processed. Therefore, mycotoxins can potentially form on the oats depending on the moisture content, storage conditions and time.

The difficulty with assessing the formation of mycotoxins in cereals in an industrial setting is the ability to achieve representative sampling because samples will need to be taken over a prolonged period of time. The impact of processing on mycotoxins has been previously investigated in commercial UK cereal mills by Scudamore and co-workers showing that 90-95% of Fusarium mycotoxins are eliminated from oats during the production of oat flakes. The study showed that reduction up to 99% of mycotoxins
can be achieved at higher levels of contamination.