Pests and diseases can cause severe losses to greenhouse crops and are often the most visible problem that growers encounter. The protected greenhouse environment favours the presence of a number of pests and the warm, humid greenhouse environment can also favour a number of plant pathogens (disease-causing organisms) that can infect plants and fruit. Losses from pests and diseases occur directly through reduced yields. Many pests, such as whiteflies and thrips can also spread viruses.

Good agricultural practice (GAP) in greenhouse pest and disease management is reliant on good crop hygiene practices and fast, correct diagnosis of any unfamiliar or unusual plant symptoms.