Cause of Fusarium head blight (FHB) in organic winter rye protected by biopreparations and contamination of the grain with the deoxynivalenol, T-2 toxin, zearalenone, aflatoxins and ochratoxin A were analysed. Biochicol 020 PC and biopreparation made in laboratory on the ground chitosane and Fusarium culmorum were used in field experiment. Content of mycotoxins was defined by enzyme-linked immunosorbent assay (ELISA). Main cause of triticale head blight were Fusarium culmorum, Fusarium graminearum and Fusarium poae. From grain of protected objects higher numbers of Fusarium spp. were isolated than in control. Among 13 of the examined cultivars of organic rye deoxynivalenol was identified in some cultivars protected by biopreparations and in control objects. Zearalenone was detected in majority of cultivars in all objects. Own biopreparation stimulated accumulation of deoxynivalenol and zearalenone in grain of some cultivars. T-2 toxin and ochratoxin A were detected sporadically, but aflatoxins were not found in triticale grain.