Eight triticale genotypes, naturally contaminated (C) and collected from heads inoculated with two separate isolates Fusarium culmorum (I1 and I2) kernels were analysed for accumulation ofFusarium toxins. Triticale kernels were contaminated with deoxynivalenol (DON) and 3‐acetyldeoxynivalenol (3‐AcDON). Statistical analysis revealed significant differences between naturally contaminated samples (C) and those inoculated with isolate I1 and I2. The following accumulation of toxins in kernels (mean mg/kg) was found: C, I1, I2 – DON 0.06, 14.45, 8.09; 3‐AcDON – 0.01, 0.20, 0.49. Distribution of DON and 3‐AcDON was studied in four size fractions of kernels (> 2.8 mm; ≤ 2.8–2.5 mm, < 2.5–2.2 mm and < 2.2 mm).The highest concentration of DON and 3‐AcDON was found in the smallest fraction of damaged kernels. The percentage distribution of DON and 3‐AcDON in fraction < 2.2 mm was (C) 66%, 77%, (I1) 38%, 27%, (I2) 46%, 40%; and in fraction < 2.5 mm: (C) 85%, 94%, (I1) 57%, 51%, (I2) 80%, 76%. The naturally contaminated kernel fraction < 2.2 mm (although only 2% of all) contained 33% DON and 59% 3‐AcDON, for more toxigenic isolate I1 10%, 15%, 14%, less toxigenic isolate I2 4%, 13%, 11%, respectively, calculated on dry matter basis. No significant correlation between examined characteristics was found for either I1 or I2 isolate. The biosynthesis mechanism of toxic metabolites was to approximate (significantly correlated) to pair objects C/I2.