Aspergillus and Penicillium are ubiquitous fungi, usually found as saprophytes. Only a few species are considered to be important in human or animal disease. However, many otherwise benign species are supreme opportunists and have been found increasingly as invaders of the immuno-compromised. This paper first describes with a broad brush modern approaches to the classification of these genera, the reasons behind some name changes and the effective forces now acting to stabilize names. Recent taxonomic schemes are described. The taxonomy of pathogenic Aspergillus and Penicillium species is outlined, the subgenera where pathogens occur identified, and the question of why particular species are pathogens addressed. The significance of Aspergillus and Penicillium in mammalian disease is heightened by their production of potent mycotoxins. The importance of Aspergillus flavus and aflatoxins as a cause of human death in parts of Africa and Asia and the impact of ochratoxins, produced by Penicillium verrucosum, on human and animal health in Europe will be emphasized. Possible mycotoxin ingestion from spores poses a further health threat.