Concentrations of the mycotoxins deoxynivalenol (DON) and fumonisin B1 in grain were compared among Bt-transformed corn hybrids and their non-Bt isolines on 102 commercial corn fields across Ontario from 1996 to 1999. Intensities of naturally occurring populations of Ostrinia nubilalis were assessed from tunneling measurements in the stalks of non-Bt isolines in 1996 and 1997. Mean concentrations of fumonisin B1 across hybrids were <0.25 μg g-1 in every year of the study. Relationships between the concentration of fumonisin B1 and intensity of O. nubilalis or with the use of Bt corn hybrids could not be determined because the concentrations of fumonisin B1 were below the lower limit of detection in most fields (<0.1 μg g-1). However, DON was more prevalent with mean concentrations across fields from 0.42 μg g-1 in 1997 to 1.12 μg g-1 in 1999. The effect of Bt hybrids on reducing concentrations of DON was mainly dependent on the intensity of O. nubilalis in each field. Where a high intensity (stalk injury) of O. nubilalis was observed (>4 cm of tunnel per stalk in the non-Bt), the use of Bt hybrids reduced concentrations of DON by an average of 59% from concentrations in the non-Bt isoline. Where the intensity of O. nubilalis was low (<4 cm of tunneling per stalk), concentrations of DON were not different among Bt and non-Bt hybrids. Concentrations of DON were low and not different between events Bt11 and 176 among Bt hybrids. A quadratic relationship was developed showing that the concentration of DON increased with intensity of O. nubilalis feeding. This study cautiously supports the use of Bt corn to reduce the risk of high concentrations of DON at harvest in Ontario.