Mycotoxins occurrence in wheat grains impose risks to human and animal health. The southern Brazil has favorable weather conditions for Fusarium graminearum infections and consequently for mycotoxins accumulation on grains. The goal of this study was to evaluate the behavior of new wheat commercial genotypes to Fusarium Head Blight (FHB), to control performance of new fungicide formulations and their relationship with mycotoxins concentration in grains. The manly mycotoxin occurrence on wheat grains in southern Brazil was deoxynivalenol (DON). Two cultivars showed high DON concentration above the tolerance limits (>3000 μg kg). Many other mycotoxins monitored presented concentrations below method detection limit. Satisfactory levels of fungicide effectiveness were achieved against F. graminearum. Some fungicides promoted a satisfactory decrease on DON accumulation in grains. The best results were obtained when prothioconazole was present. SDHI (Succinate dehydrogenase inhibitors) + QoI (Quinone outside inhibitors) fungicides showed benefic effects at FHB control at field, but it did not promote satisfactory reduction on DON contamination. Fungicides can be used satisfactory for FHB control and reduce DON contamination in grains in southern Brazil. The presence of prothioconazole should be recommended. Some genotypes showed high DON concentration and it was not directly related with FHB severity at field.