Last year intense rainfalls and moisture conditions were beneficial for the Fusarium sp. in Hungary. Fusarium strains decrease cereal quality (for example maize), furthermore may cause yield loss. Due to the toxin production, the fungi have a dangerous animal and human pathogen effect (Placinta et al., 1999).The effects of the Fusarium infection and its mycotoxin production haven’t been perfectly eliminated. Fusariumgraminearum is the most common agricultural pathogen in Hungary. The utilization of infected maize as an alternative biogas raw material may be an efficient and environmentally friendly disposal method. In this case, Fusarium-, and mycotoxin-content of the maize have to be analyzed as well as the impact of these factors’ on the biogas production process. Our experience was based on the raw material basis of a biogas plant. Different amount of Fusarium free and infected maize grits have been added to the regular raw material mixture. The detection of Fusarium fungi has been analyzed in experimental digesters throughout the different stages of mesophilic digestion. In the biogas liquid end product the Fusarium was detected by breeding and by microscope. According to our results, the Fusarium sp. was not detectable in the liquid end product after 30 days.