Our understanding of disease emergence is largely limited by the assumption that disease emergence is the result of increased exposure to pathogenic agents. Pathogen exposure is thought to arise through an increase in the number of interactions between humans and their natural environment, changes in demography and mobility, or through genetic variation in the infectious agents which may alter virulence or ability to infect new host species. The study of new diseases (which are often revealed by unusually severe symptoms or atypical epidemiological patterns) applies the most effort to the research of new pathogens. Here, using examples, we discuss alternative but non-exclusive mechanisms that may either reveal the presence of long-term circulating pathogens or explain changes in their nosologic properties in relation to their pattern of circulation and infection conditions. A better understanding of the ecology of pathogenic organisms and their host populations should help to define more efficient health management strategies.