The objectives of this study were to investigate the impact of Fusarium culmorum infection and fungicide application on malt quality of two domestic wheat genotypes, Lucija and Osk.110/09. Wheat genotypes were subjected to four different field treatments: control/natural conditions (1), fungicide treatment (2), inoculated with F. culmorum spores and treated with fungicide (3), and inoculated with F. culmorum spores (4). Lucija was a less susceptible genotype to Fusarium infection, in contrast to Osk.110/09, which showed off as a more susceptible genotype. Standard malting procedure for wheat malt was implemented followed by quality and mycotoxins analysis. Results indicated that malt quality varied, depending on the genotype and applied treatment, but overall conclusions indicate that genotype Lucija is more appropriate for malting, and fungicide treatment efficiently improved malt quality.