Transgenes introduced into commercial corn hybrids and soybean varieties have had limited but important indirect effects on diseases. The most clearly demonstrated effect has been related to transgenic protection against Lepidopteran insect pests of corn. Interactions between these insects and fungal pathogens are important in corn production, and the use of the Bt genes has therefore altered the risk of some diseases that affect the stalks and ears. This has resulted in reduced risk of accumulation of certain mycotoxins, primarily fumonisins. The various Bt events that have been commercialized differ in their impacts on mycotoxin risk. Because direct native resistance to mycotoxin-producing fungi is incomplete, the risk reduction associated with Bt corn cultivation can be a very important component of a mycotoxin management program. Transgenic approaches have been developed for directly reducing mycotoxin concentrations in planta, but none have been commercialized.  Indirect effects (both positive and negative) of transgenes on soybean diseases have been suggested, but not convincingly demonstrated. Both public- and private-sector researchers are pursuing transgenes for direct resistance against corn and soybean diseases, and these will ultimately have a major impact on disease management in these crops.