From economic and environmental points of view, enhancing resistance to Fusarium head blight (FHB) in wheat is regarded as the best option to reduce fungal colonisation and the concomitant mycotoxin contamination. This review focuses on the effect of FHB resistance on deoxynivalenol (DON) and the masked metabolite deoxynivalenol-3-glucoside (DON-3-glucoside) in wheat. Based on published information complemented with our own results we draw the following conclusions: (1) All investigated wheat cultivars can convert DON to DON-3-glucoside. Hence, detoxification of DON to DON-3-glucoside is not a new trait introduced by recent resistance breeding against FHB. (2) The amount of DON-3-glucoside relative to DON contamination can be substantial (up to 35%) and is among other things dependent on genetic and environmental factors. (3) Correlation analyses showed a highly significant relationship between the amount of FHB symptoms and DON contamination: breeding for FHB resistance reduces DON contamination. (4) DON contamination data are highly correlated with DON-3-glucoside concentration data: in other words, reduction of DON content through resistance breeding results in a concomitant reduction in DON-3-glucoside content. (5) The DON-3-glucoside/DON ratio increases with decreasing DON contamination: the most resistant lines with the lowest DON contamination show the highest relative level of DON-3-glucoside to DON. In summary, introgressing FHB resistance reduces both DON and DON-3-glucoside levels in the grain, but the reduction is lower for the masked toxin. DON-3-glucoside can represent a possible hazard to human and animal health, especially in wheat samples contaminated with DON close to permitted limits.