This study defines several mycotoxin (Aflatoxin B1, Aflatoxin B2, Aflatoxin G1, Aflatoxin G2, Ochratoxin A, Deoxynivalenol, Zearalenone, Toxin T-2, Toxin HT-2, Nivalenol, Fusarenon X, 3-Acetyl-deoxynivalenol) contamination of winter common, durum, spelt and einkorn wheat genotypes. The compared species (Triticum aestivum ssp. vulgare, T. durum, T. aestivum ssp. spelta and T. monococcum) have different susceptibility to Fusarium and toxin accumulation. Durum wheat (cv. Komnata) was the most susceptible to contamination with mycotoxins. In durum grain the highest level of contamination was detected, especially with Deoxynivalenol (2–4 times over the allowed level for unprocessed grain). T. aestivum ssp. spelta (cv. Schwabenkorn) and T. monococcum (EN 5003) showed the lowest mycotoxin level. Triticum aestivum ssp. vulgare (cv. Tonacja) was less contaminated with mycotoxins than Triticum durum but more than T. aestivum ssp. spelta and T. monococcum. Other mycotoxins in grain of the examined genotypes occurred in trace amounts.