Deoxynivalenol (DON) is a mycotoxin found in wheat that is infected with Fusarium fungus. DON may also be converted to a type of "masked mycotoxin", named deoxynivalenol-3-glucoside (D3G), as a result of detoxification of the plant. In this study, DON and D3G were measured using gas chromatographic (GC) and liquid chromatography-mass spectrometry (LC-MS) in wheat samples collected during 2011 and 2012 in the USA. Results indicate that the growing region had a significant effect on the DON and D3G (p < 0.0001). There was a positive correlation between both methods (GC and LC-MS) used for determination of DON content. DON showed a significant and positive correlation with D3G during 2011. Overall, DON production had an effect on D3G content and kernel damage, and was dependent on environmental conditions during Fusarium infection.