One hundred and twenty-two samples of cheeses made from goat and sheep milk and a mixture of the two types, produced in Southern Italy by industrial establishments or artisans, were analysed for the detection of fungal contamination and the presence of potentially toxigenic moulds. Only organoleptically acceptable cheeses without evident fungal contamination were studied. Among these, 40 were unripened, 30 medium and 52 long ripened cheeses. Moulds were found in 54 of the 122 analysed samples (44.3%). The most contaminated cheeses were the medium and long ripened ones (46.3% and 35.2%), and the industrial cheeses (59.1%). The artisan cheeses were the least contaminated (26.8%). Among the cheeses that tested positive, Penicillium species were the most frequently isolated (72.9%), followed by Geotrichum spp. (7.3%), Aspergillus spp. (4.2%) and Mucor spp. (4.2%). The potentially toxigenic species within the genera Penicillium, Aspergillus and Fusarium were mainly detected in sheep cheeses.