The maize stalk rot complex is comprised of several fungal pathogens, including Gibberella zeae, Colletotrichum graminicola, Stenocarpella maydis, and several members of the genus Fusarium. The European corn borer (ECB) (Ostrinia nubilalis) can contribute to stalk rot development by creating entry wounds and by serving as a vector of some stalk rot pathogens, particularly Fusarium verticillioides. Transgenic insect protection of maize hybrids with insecticidal proteins derived from Bacillus thuringiensis greatly reduces ECB injury and may therefore alter the species composition and diversity of the stalk rot complex. Field experiments were conducted in 1998, 1999, and 2000 to compare the species composition and diversity of fungi infecting stalks of Bt and non-Bt maize hybrids. Hybrids representing five Bt types (or "events") and their near-isogenic non-Bt counterparts were subjected to manual and natural infestations with ECB larvae. Stalk tissue samples were cultured to determine fungal species composition. At least one species was isolated from nearly every stalk and from both diseased and symptomless tissues. G. zeae was the most common species in 1998 and 1999, but C. graminicola was most common in 2000. The mean proportions of stalks infected with F. verticillioides, F. proliferatum, and F. subglutinans were significantly lower in Bt hybrids than in non-Bt hybrids in 2 of the 3 years. Conversely, the mean proportion of stalks infected with G. zeae was higher in some Bt hybrids than their non-Bt counterparts in two of the three years. F. verticillioides was more likely to be isolated from ECB-injured tissue, whereas G. zeae and C. graminicola were more likely to be isolated from tissue not associated with ECB injury. The overall species diversity of the stalk rot complex was lower in some Bt hybrids compared with their non-Bt counterparts in 1998 and 1999. ECB activity appeared to alter fungal species composition in stalks, reflecting the association between ECB injury and specific stalk rot pathogens, particularly F. verticillioides. The species composition of fungi infecting stalks of Bt hybrids differed from that of non-Bt hybrids, but the implications of this result are not yet clear.