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The occurrence of toxins produced by Fusarium species in cereals and other agricultural commodities has increasingly raised interest over the last two decades. Efforts were mainly directed to the occurrence of zearalenone, an estrogenic Fusarium metabolite and to toxic trichothecenes (deoxynivalenol, nivalenol, T-2 toxin, HT-2 toxin, diacetoxyscirpenol). The occurrence of Fusarium toxins in barley grown in southwest Germany has been monitored by thin layer chromatography (TLC) and gas chromatography (GC) with FID or ECD detection. However, TLC is not sensitive enough to detect low levels of Fusarium toxins and confirmation is difficult, whereas GC method with FID and/or ECD can yield false positive results in extracts obtained from agricultural commodities for trichothecenes. In the present study, we used a gas chromatograph equipped with a mass selective detector, which is a sensitive and confirmatory method to determine Fusarium toxins in cereals. Barley samples were collected soon after harvest because preharvest contamination is of main interest for agricultural practice. The kernels were microbiologically examined for invasion by Fusarium, as well as by Penicillium and Aspergillus species, since these latter two have been described as storage fungi.