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Testing of the presence of toxigenic microfungi and mycotoxins in foodstuffs in the food chain is an important part of the food safety strategy in The Czech Republic. At the national level, control of their presence in the entire food chain is assured by Public Health Protection Agencies, by the Veterinary Administration and by the Czech Agriculture and Food Inspection Authority. This article summarizes surveillance activities of Public Health Protection Agencies and mycotoxins findings in dietary raw materials and foodstuffs from the 1990s to 2004 in the Czech Republic. At present, the health risk from the mycotoxins exposure from foodstuffs is assessed to be relatively low in the Czech Republic, especially as far as the foodstuffs of the Czech origin are concerned. It may result in late toxic effects (e. g., carcinogenic risk) following a single or repeated ingestion of low mycotoxins doses from foodstuffs. Nevertheless, the overall situation may change due to the globalization of the food market. In order to minimize the risk associated with mycotoxins and eliminate their impact on Czech public health, continuous monitoring of the presence of toxigenic moulds, mycotoxins, and their biomarkers is necessary, in conjunction with strict respect to European Union legislation.