Contamination by toxigenic fungi and their mycotoxins of agricultural products grown in Europe is a problem, and dramatic differences in environmental conditions in various European countries significantly influences the distribution of toxigenic fungi and related mycotoxicological risks. Emerging problems due to climate change and new mycotoxin/commodity combinations increase these concerns. Trans-global transposition and trade exchanges of plant products also contribute significantly to the spread of toxigenic fungi worldwide and represent an important source of inoculum for new plant diseases in Europe and for broadening the genetic diversity of already existing local populations. We illustrate the major problems associated with mycotoxin contamination of agricultural products in Europe by focusing on three crops and their relevant diseases: (i) wheat with Fusarium head blight and Penicillium infections, (ii) maize with Fusarium ear rot and Aspergillus infections, and (iii) grapes with black Aspergillus rot.