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Wheat (Triticum aestivumL.) is an important cereal crop in Kosovo and a major component of population food. Fusarium head blight (FHB) of wheat is an economically very significant disease. FHB leads to various losses in quality like reduced germination of seeds, reduced baking quality and reduced nutritional quality through mycotoxin contamination. In 2010 and 2011 the incidence and identity of the Fusariumspp. infecting wheat in Kosovo as well as mycotoxin contamination was investigated. The results of two years research work show that the incidence of FHB on winter wheat in 2010 was low (<6%). In the year 2011 the disease incidence was clearly higher (up to 31%). Based on morphological characters, F. graminearumwas the most frequently Fusariumsp. identified on wheat kernels in the year 2010 (100%) and 2011 (98%). Less frequently isolated species included F. cerealis(<1%) and F. avenaceum(<1%). Wheat flour samples were analyzed by liquid chromatography coupled to mass spectrometry and found to be contaminated with a variety of mycotoxins, most importantly deoxynivalenol and zearalenone. This is the first report on the incidence as well as on the identification of Fusariumspecies isolated from naturally infected winter wheat in Kosovo.