The objectives of this study were to establish the impact ofFusarium culmorum infection and fungicide treatment on the occurrence of deoxynivalenol (DON), 3-acetyl deoxynivalenol, T-2 toxin, HT-2 toxin, nivalenol, fusarenon-X, diacetoxyscirpenol and zearalenone in wheat, wheat malt and wort (beer). The concentrations of these compounds were also measured in the germ/rootlets, spent grains and spent yeast because these are the most important by-products and are further used as food or feed additives. Two wheat genotypes were obtained from the Agricultural Institute in Osijek, Croatia. The Osk.110/09 genotype, the genotype more susceptible toFusarium infections, and Lucija, the genotype less susceptible toFusarium, were analysed in this research. Each genotype was treated in four different ways at the field: (A) control, (B) treated with fungicide Prosaro® 250, (C) inoculated withF. culmorum spores and treated with fungicide Prosaro® 250, and (D) inoculated withF. culmorum spores. All samples were malted and brewed according to standard procedures, products and by-products were analysed for the mycotoxins by using LC-MS/MS. Since the majority of trichothecenes are polar molecules, the water after steeping was also analysed with LC-MS/MS. Mycotoxin concentrations were lower in malt samples treated with the fungicide. Elevated mycotoxin concentrations were observed in samples of both genotypes exposed toF. culmorum. Fungicide treatment was observed to suppress mycotoxin production and accumulation. However, samples with notably high mycotoxin concentrations, especially DON, retained elevated mycotoxin concentrations throughout the entire beer production process, even after a six-month storage period. DON proved to be the most frequently occurring mycotoxin in all of the by-products. The highest concentration of this compound was found in the steeping water from sample D (Osk.110/09), at 20,326 μg/l, leaving the spent grains of this sample with no detectable levels of DON.