Experiments conducted at the Lithuanian Institute of Agriculture in 2004–2005 were designed to investigate the contamination of winter rye cv. ‘Duoniai’ and triticale cv. ‘Tornado’ grain with fungi of genus Fusarium and mycotoxins produced by them as affected by the spray-applications of the crops with the fungicides propiconazole, tebuconazole, and azoxystrobin at the beginning of anthesis (BBCH 63). Having analysed winter rye and triticale grain samples for Fusarium species composition (Fusarium avenaceum (Fr.) Sacc, F. sporotrichioides Sherb., F. poae (Peck) Wollenw, F. culmorum (W. G. Sm.) Sacc., F. graminearum Schwabe, F. solani (Mart.) Sacc., F. incarnatum (Desm.) Sacc . F. sambucinum Fuckel) were identified in rye grain — (F. culmorum (W. G. Sm.) Sacc., F. poae (Peck) Wollenw., F. heterosporum Nees) — in triticale grain. The grain samples from winter rye plots sprayed with azoxystrobin were the most heavily affected by Fusarium (42.5%) and the highest contents of DON (691 μg kg−1) and T-2 toxin (153.6 μg kg−1) were identified in them. Tebuconazole reduced the amount of Fusarium-affected grain in rye and triticale, but did not have any effect on mycotoxin production in rye. The grain of triticale not sprayed with fungicides was more heavily contaminated with DON (427 μg kg−1).