This paper is willing to make a comparison regarding the content of mycotoxins in bakery wheat from different Transylvanian districts, the results being obtained in the climatic conditions of the years 2005 and 2006. The wheat samples were taken from Alba, Cluj, Covasna, Hunedoara, Sălaj and Timiş district. It was analyzed the content in Ochratoxin A, Aflatoxins B1, B2, G1, G2 and total aflatoxins from the flour obtained by milling the wheat seeds, using the method of thin layer chromatography. As a general trend, it was observed a decreasing content in mycotoxins in 2006 towards the year of 2005. The only district that invalidates this trend is Sălaj district.