Increased photosynthetic carbon assimilation rate in C3 crops, such as wheat, at elevated atmospheric CO2 concentrations can dramatically alter grain nutritional quality. Typically, growth at elevated CO2 leads to grain with higher carbohydrate content which in turn also significantly alters the protein, mineral and lipid compositions. The production of the mycotoxin, deoxynivalenol (DON), by F. graminearum is highly dependent on the nutrient composition of its growing medium. Therefore, alterations in the nutritional composition of wheat when grown under conditions of elevated CO2 likely have a significant impact on F. graminearum infection. This investigation explores how changes in wheat primary metabolism due to elevated CO2 affect F. graminearum growth and DON production. Additionally, the impacts of growth at elevated CO2 on grain nutritional quality of moderately resistant and susceptible wheat varieties were compared and found to be significantly different.