Mycotoxins are secondary metabolites produced by a number of fungi that make part of soil biota in agroecosystems. Their overall adverse effects comprise structural and functional alterations of vital organs, carcinogenesis, allergic reactions and acute toxicosises. Therefore, mycotoxin concentration in foods is strictly regulated in many countries. Timely identification of mycotoxin producents in crop yield significantly decreases the emerging risks of foodstuff contamination and impact on human health as a result. PCR is an effective and fast method of plant screening for the presence mycotoxin-producing fungi due to its reliability, high specificity and rapidity. Current paper outlines the fungal genome sequences implicated in mycotoxin synthesis: fumonisin gene cluster, patulin biosynthetic gene cluster and others used for primer design for PCR and nested-PCR. Obtained results show the dynamics of mycotoxin-producing fungi propagation in maize plants depending on plant genotype and phase of vegetation. Most common species from Fusarium, Aspergillus, Penicillium and Myrothecium genera that infest maize plants and are associated with mycotoxin production during vegetation are shown.