A survey was undertaken to determine the mycoflora associated with stored wheat in four states across Australia including Western Australia, South Australia, Victoria and New South Wales. A total of 482 fungal isolates from 15 genera were isolated. The most common genera isolated were Alternaria spp., Aspergillus sp., Aureobasidium sp., Cladosporium spp., Drechslera sp., Fusariu m spp., Mucor sp., Nigrospora sp., Penicillium sp., Rhizopus sp., Stemphylium sp., Eutiarosporella sp p., Ulocladium sp., Epicoccum sp., and an undescribed genus from the Hypocreales. Diversity profiling also identified fungi that were not isolated using traditional methods including Paecilomyces spp., Dendryphiella and Cryptococcus. The results indicate that the mycoflora of stored wheat varies between Australian grain growing regions, and that diversity profiling analysis identifies different fungal contaminants compared to traditional methods. This study also revealed that some pathogens of high risk to humans (e.g. Cryptococcus) may occur with a high frequency in wheat.