Emerging mycotoxins are of a great importance due to their high occurrence in foods and feeds and their implication in pathologies. There is a need to control them both in pre- and post-harvest. However, the increasing drawbacks of chemical decontamination methods, makes the use of preventive methods more attractive. These are based on avoiding growth of mycotoxigenic fungi and mycotoxin accumulation in these substrates (by using reduced aw levels, and modifying other storage conditions) and the early detection of these mycotoxins by using simple and fast analysis techniques. At the same time, it is important to know the effect that industrial processing has on mycotoxin concentration in foods and feeds, because it may reduce the toxin content. Finally, maximum limits of mycotoxin concentration should be established for both foods and feeds.