The aim of this paper is to enumerate and explain the roles of secondary metabolism of mycotoxigenic moulds and to say a few words about the products of secondary metabolism. Some moulds have the ability to synthesize mycotoxins, toxic products of the secondary metabolism with a low molecular mass. Unlike the primary metabolism, secondary is not essential for growth and development of a specific mould, but it does ensure them a protection against competitors and predators, adaptation to numerous environmental conditions, nutrient acquisition, etc. Moulds secondary metabolites have diverse applications in medicine, pharmacy, food technology, etc. because of their antibacterial, antifungal, anticancer, hypocholesterolemic and antiviral biological activites. However, some of them can cause more or less dangerous mycotoxicoses because of their many toxic features. They are very important for the economy of some countries because moulds mainly contaminate market crops, which cannot go to the market if they are contaminated. Fot these reasons mycotoxins have become the subject of many researches. The most important genuses of mycotoxigenic fungi are Alternaria, Aspergillus, Fusarium and Penicillium, and some of the most important mycotoxins are aflatoxins, citrinin, ergotamin, fumonizins, ochratoxins, patulins, trichotecens and zearalenons. From these groups of mycotoxins, aflatoxins are by far most important because they are the most abundant and the most toxic and can be often refered to as mycotoxins in general.