This paper reviews the challenges relating to chronic contamination of small grains and maize with deoxynivalenol and related compounds, fumonisin and the use of ensiled cereals in cool dairy areas. Uncertainties in the tolerable daily intakes for deoxynivalenol and fumonisin are discussed as they have the potential to affect current regulatory limits. In addition, climate change is resulting in more extreme rainfall and drought events which favour formation of deoxynivalenol and fumonisin, respectively. The development and refinement of models for predicting mycotoxin accumulation from weather data will become an essential tool for managing these events. Such models are also important for providing timely food aid to developing countries, which experience increased occurrence of acute toxicities, especially in children. Chronic contamination of silage in some areas with some Penicillium toxins deserves more attention in terms of their economic effects and possible implications for the purity of milk.