Versatile microbiota are inevitably naturally present on cereals. Fungi, yeasts and bacteria and their metabolites all contribute to the quality and safety of the final products derived from most common beer cereals-barley and wheat. The microorganisms that are most often associated with the safety and quality of cereals for beer production belong to the Fusarium spp. They greatly influence yields from the field, and can modify and diminish economic success for farmers. However, the real problem is their harmful metabolites-mycotoxins-that affect the health of humans and animals. In the era of emerging analytical methodologies, the spectrum of known toxins originating from microorganisms that can pose a threat to humans has grown tremendously. Therefore, it is necessary to monitor microflora throughout the productive "barley to beer" chain and to act suppressive on the proliferation of unwanted microorganisms, before and during malting, preventing the occurrence of mycotoxins in final products and by-products. Multi-mycotoxin analyses are very advanced and useful tools for the assessment of product safety, and legislation should follow up and make some important changes to regulate as yet unregulated, but highly occurring, microbial toxins in malt and beer.