Many species of Fusarium fungi can produce a number of different mycotoxins including trichothecenes such as deoxynivalenol (DON), nivalenol (NIV), zearalenone (ZEA) and others. The farming system have an effect on quality of grown plants, including mycotoxin contamination. The contamination of winter wheat (Triticum aestivum L.) and rye grain by toxins with focus on the genus Fusarium was monitored within the years 2009 -2011 under the official control according to EC Regulation 401/2006 and 178/2010 on the territory of the Slovak Republic in organic and conventional grains. The concentration of deoxynivalenol (DON) was determined by HPLC/DAD detector and concentration of zearalenone (ZEA) by HPLC/FLD detector. Results of analysed samples showed that DON was the most prevalent Fusarium toxin. In the analysed samples were observed significant differences between organic and conventional wheat samples. Results showed that samples from organic production contained significantly lower contamination of DON and ZEA mycotoxins than from conventional production. In four wheat samples from conventional production was the content of DON over the EC Regulation no. 1881/2006 about setting the maximum levels for certain contaminants in foodstuff. Within the observed period, the highest DON concentrations were observed in the year 2010, in both wheat and rye samples, and organic and conventional production. The year 2010 was characterised by constant rain, moist soil on the most area of Slovakia. Since lower contamination of Fusarium toxins was found in wheat and rye from organic farming, it can be concluded, that factors related to agricultural practices in this system can reduce the risk of Fusarium mycotoxin contamination.