Greenhouses are intensive cropping systems where microclimatic conditions are particularly favourable for the development of different fungal diseases (fungal-like organisms and true fungi) and if no proper control measures are taken in time, losses may be high. The principal fungal diseases are presented, as well as examples of emerging or re-emerging diseases, which may represent, in the future, a major threat to greenhouse production in some areas. Examples of fungal diseases are given based on their specificity towards target plant organs (aerial organs, vascular system, roots/collar). This chapter provides information relevant to the diagnosis, biology of the main fungal plant pathogens and the epidemiology of the diseases encountered in such greenhouse cropping systems. Basic information on plant protection methods is also provided: control strategies of fungal diseases still rely on the use of chemicals but transition to integrated pest management (IPM) is in progress in many countries worldwide.