Botrytis elliptica, the pathogen causing 'lily disease' produces black, seed-like resting structures (sclerotia) in dead leaf tissue and in this form overwinters in the soil, releasing airborne spores the following season. Wet conditions are needed for infection. The pathogen is closely related to other Botrytis species which attack specific hosts (e.g. B. galanthina on snowdrops).
There are many host-specific strains of the soil-borne fungal pathogen Fusarium oxysporum, and the one known as Fusarium oxysporum f. sp. lilii only attacks lilies. It often enters through the basal plate, especially if this is damaged. It can contaminate the soil for at least three years in the absence of lilies. The fungus Rhizoctonia solani is very common and widespread and exists as many different strains. It is serious on tulips, less so on lilies, bulbous iris, ixias, colchicums, crocuses, hyacinths and narcissi. This fungus also produces sclerotia, which allow it to persist in the soil for several years.
Tulip breaking virus is carried from plant to plant (vectored) by aphids. Other viruses such as Cucumber mosaic virus also affect lilies and often more than one type of virus can be present in the same plant, leading to very variable symptoms. Because lilies are perennial, virus infection tends to accumulate with age.