The aim of this study was to determine the profile of fungal metabolites and antioxidant substances from plants on a representative population of wheat cultivars grown in Poland. Tests were conducted on grain of 23 wheat cultivars in three experimental variants: natural infection (control), chemical crop protection, and artificial inoculation with the fungi F. graminearum and F. culmorum. Grains were analysed in terms of infection rate, mycotoxin, ergosterol, free and bound phenolic acid content, as well as antioxidant capacity. Calculated Fusarium head blight index (FHB index) ranged from 0% to 24% in the control, from 0% to 95% after inoculation and from 0 to 3% following chemical crop protection treatments. The highest concentration of ergosterol was detected in seeds from inoculated plots, with a mean value of 26.69 mg/kg. The highest mean concentration calculated for total toxin content was recorded after inoculation (7.833 mg/kg). The mean value for ferulic acid for inoculated samples resulted 2574 mg/kg, while for chemically protected samples 1158 mg/kg was obtained.Based on of discriminant analysis genotypes can be separated for inoculation 100%, for chemical crop protection 95%, and for natural infection 90%. Amongst 12 analysed phenolic acids the highest discrimination power was found for gallic acid, 4-hydroxybenzoic acid and vanillic acid.