The development and use of tolerance have been proposed as an alternative or complementary method to host resistance in the management of plant diseases, including those caused by viruses. There has been much ambiguity among plant pathologists, plant breeders, and agronomists in the meaning of tolerance and how it can be operationally defined, but a modern consensus seems to have emerged. Tolerance is a relative term that means a limited reduction in host plant fitness (reproduction or survival) in relation to pathogen load throughout or during a defined period of plant development and growth such as the reproductive stage. This emphasizes the need to study reproductive stage disease tolerance. Despite this apparent consensus, there remain questions over the use of model plant systems, the genetic background of tolerance, its physiological expression, and epidemiological consequences of its deployment in crops, in comparison with host resistance. Most examples of tolerance reviewed here are for plant virus systems, although other pathogen taxa are referred to, as is tolerance as a natural phenomenon in wild plants including crop relatives. An argument is made for studying commonalities and interactions in host responses to biotic and abiotic stressors; in particular, whether virus infection can mitigate the impact of heat, cold, drought and salinity stress in plants. Finally, we review the use of mathematical models as a means of evaluating the strategy of using tolerance in disease and crop management.