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As determined by the Intergovernmental Panel on Climate Change, warming of the climate system is unequivocal and has been associated with rising sea levels, diminished amounts of ice and snow and increasing oceanic and atmospheric temperatures. Such climate changes have a significant impact on stages and rates of toxigenic fungi development and can modify host-resistance and host-pathogen interactions, influencing deeply also the conditions for mycotoxin production that vary for each individual pathogen. Moreover, the new combinations mycotoxins/host plants/geographical areas are arising to the attention of the scientific community and require new diagnostic tools and deeper knowledge of both biology and genetics of toxigenic fungi. In this review, it is underlined that an extension of the aflatoxin contamination risk in maize in South and Central-Europe is highly likely in the next 30 years, due to favorable climatic conditions to the growth of Aspergillus flavus. Moreover, the mycotoxigenic Fusarium species profile on wheat in Europe is in continuous change in Northern, Central and Southern-Europe with, in particular, a worrisome growing contamination of F. graminearum in the Central and Northern Europe.