Fusarium infection level, DNA quantity of the Fusarium poae, F. sporotrichioides, F. langsethiae, F. culmorum, F. graminearum and F. equiseti as well as deoxynivalenol (DON), zearalenone (ZEN ) and T-2 toxin (T-2) content were investigated in grain from cultivars of different cereal species grown on organic farming sites during 2005-2006. The Fusarium infection level was examined by agar plating of single grains, Fusarium spp. DNA content was determined by real-time PCR and the mycotoxins were analyzed by ELISA. Almost all cereal grain samples grown under organic conditions were infected by Fusarium spp. The grains of winter cereals were less infected with Fusarium compared with those of spring cereals. The presence of F. culmorum, F. equiseti, F. sporotrichioides, F. poae, F. langsethiae in cereal grain depended on the environmental conditions during the experimental years. Higher Fusarium species diversity was found in 2005 when the conditions were more favourable for Fusarium infection in cereal grain, whereas F. poae and F. langsethiae were prevalent in cereal grain in 2006. F. langsethiae, identified in Lithuania for the first time, was more frequent in spring cereals than in winter cereals. Almost all grain samples were found to be contaminated with DON, ZEN, T-2 at low concentrations; however, it is known that the action of toxins at low concentrations is slow, the adverse effects are evidenced only after some time and in different forms, which poses a serious risk to human and animal health.