Projected climate change effects will influence primary agricultural systems and thus food security, directly via impacts on yields, and indirectly via impacts on its safety, with mycotoxins considered as crucial hazards. Mycotoxins are produced by a wide variety of fungal species, each having their own characteristics and requirements. The geographic distribution of toxigenic fungi reflects their ecological needs, with thermophilic fungi prevalent at lower latitudes and psychrophiles at the higher latitudes. A resulting gradient of mycotoxin contamination has been repeatedly stressed. Changes in climatic conditions will lead to shifts in the fungal population and the mycotoxin patterns. In general, climate change is expected to increase mycotoxin contamination of crops, but due to the complexity of mycoflora associated to each crop and its interaction with the environment, it appears rash to draw conclusions without specific studies. Very recently first quantitative estimations of impacts of climate change on mycotoxin occurrence have been made. Two studies each applied models of different disciplines including climate projection, crop phenology and fungal/mycotoxin prediction to cereals cultivated in Europe. They were followed by a case study on climate change effects on Alternaria moulds and their mycotoxins in tomato. Results showed that DON contamination of wheat grown in Europe was, in general, expected to increase. However, variation was large, and in some years and some regions a decrease in DON contamination was expected. Regarding aflatoxin contamination of maize grown in Europe, an increase was estimated, mainly in the +2 °C scenario. Two main research gaps were identified related to the (limited) number of existing quantitative models taking into account climate change and their validation in limited areas. Efforts are therefore mandatory to be prepared for future changes and challenges on model validation and limited mycotoxin-crop combinations.