Research on the epidemiology of plant diseases is briefly reviewed, focusing on two diseases caused by mycotoxin-producing pathogens: Fusarium ear (or head) blight (FEB or FHB) of small grain cereals and apple blue mould (Penicillium expansum). Pathogen development during its key life cycles is discussed in relation to important environmental factors and host resistance. Current control methods are also reviewed, focusing on cultural and biological methods. The future challenge is to understand the relationships between disease severity, fungal biomass and the production of associated mycotoxins in order to minimize risks of both disease damage to crop yields and threat to human health posed by mycotoxins.