The aim of the work was determination of the spectrum of filamentous fungi in hybrid grains maize (Zea mays L.) harvested in 2009 from four sites representing the main growing area of grain maize in the Czech Republic. The intensity of fungal infection of grains from conventional hybrids and Bt-derived versions was compared in the experiment Microbiological method was used for identification of pathogens. The maize grains were infected by Nigrospora (48.9%), Fusarium (24.3%), Alternaria (23.3%) and Cladosporium (1.8%), in average. Sporadic occurrence has been reported in the genus Mucor (0.5 %), Penicillium (0.4%), Chaetomium (0.4%) and Trichoderma (0.3%). Less fungal isolates were isolated from grains of Bt-version, generally. There were not found any statistically significant differences in the number of isolates of the fungal genera Alternaria, Fusarium, Cladosporium, Mucor, Penicillium, Chaetomium and Trichoderma occurring on traditional hybrids and their Bt-version. Statistically significant differences between several samples were determined in the genus Nigrospora, only. Information concerning occurrence of fungi on maize grains are important in prevention of deterioration in quality and quantity of harvested production.