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This review was inspired by an apparent oversight. A report claimed that a gene probe based on a regulatory gene for aflatoxins could be used selectively for screening foodstuffs. However, aflR also regulates sterigmatocytin production so that many other fungi could provide a positive result. I suggest that aflP, or aflQ are more logical choices. Other aspects are reviewed including why it is valid to screen for the metabolic pathway rather than marker DNA, and emphasising that the current state of fungal taxonomy does not permit absolute confidence in delineations of taxa. Also, the gene sequences determined from very few strains may not represent the situation in nature. Common genes for a wide range of important mycotoxins (e.g. polyketide synthetase) may not be able to be used with authority, and more specific ones are desirable (e.g. isoepoxydon dehydrogenase). Metabolomics may challenge PCR analysis under certain circumstances and the most appropriate technology needs to be considered. Negative PCRs can be false. Quantifying fungi is a surprisingly inaccurate science, and also in relation to mycotoxin concentration. It is noticeable that few strains of taxa have been investigated in many cases. PCR of mycotoxigenic Aspergillus, Fusarium, and Penicillium i