Wheat and wheat products are frequently subjected to mould infestations. Many of them are potential producers of various mycotoxins. Some of the consequences, due to the infestations by genus Fusarium and Alternaria, are mostly: yield loss, decrease of biological and technological quality, and unacceptable quality of infected kernels for the production and processing into human food because of the possible presence of mycotoxins. It is unknown whether and how the contaminated grains are distributed during milling into various flour streams and finished products. Wholegrain flours and related products contain all anatomic parts of kernels, including mycotoxins. It is a known fact that mycotoxins are resistant to thermal degradation, so they do not loose their toxicity during processing. Moulds from genus Fusarium spp. and Alternaria spp. synthesize mycotoxins, mostly zearalenon and ochratoxin A. The aim of the investigation was to examine mould contamination of wheat grain, as well as to identify the isolated species, especially those capable of producing toxins, and to determine their impact on technological quality, safety and sanitary condition of wheat. Six varieties of wheat, contaminated with moulds, were investigated. Each sample was separated manually into four fractions: sound kernels, black germ kernels, kernels infected slightly and those infected severely with Fusarium spp.