DIMBOA (2,4-dihydroxy-7-methoxy-1, 4-benzoxazin-3-one) has been identified as an important allelochemical in maize providing resistance to some insects and fungal diseases. However, this trait has been bred out of most modern corn varieties. Now crops have been genetically modified with the Bt (Bacillus thuringiensis) gene to enhance their insect resistance. We hypothesize that these two traits can be combined to enhance crop resistance. The objective of this study was to compare the concentration of DIMBOA in corn with and without Bt genetic modification and under different growth conditions. Five pairs of near-isogenic corn hybrids with and without genetic modification were grown under different conditions: normal (control), nitrogen deficient and limited moisture. DIMBOA concentrations were measured in young leaves from three different growth stages. Bt-protein concentrations were measured in all plants to confirm its production in the hybrids. The results showed DIMBOA concentrations increased significantly in all hybrids under the stress both stress conditions, drought or nitrogen deficiency. There was no consistent trend in changes in DIMBOA concentrations in Bt versus non-Bt counterpart under the three conditions tested. Differences in DIMBOA production in the five Bt corn varieties tested did not correlate with their Bt-protein concentrations. Implying that DIMBOA production does not compete directly with Bt-protein production and therefore it is possible to combine the two traits. However, maximum production of DIMBOA and Bt-protein appears to be variety dependent therefore further experiments are necessary to determine optimal concentrations for pest control.