Pathogens are relatively benign in undisturbed forest because trees of any one species are generally widely-spaced. When the forest is disrupted (and especially when monocultures are established), reducing diversity, pathogens and parasites can spread more easily and epidemics occur. Logging and road construction provide opportunities for the entry of pathogens into healthy trees through cut stumps or wounds, which may also attract insect pests. Many diseases become rampant in tree plantations or secondary forests which contain many trees of one species (as has happened in tea, rubber, and cocoa plantations). The witches broom fungus, a natural pathogen of cacao in the Amazon, has spread rapidly in the cacao plantations established under rainforest canopy in Brazilian Atlantic rainforest (Bright, 2001). A fungus, Botryodiiplodia theobromae, is normally present in pines, but when trees are stressed, as in a plantation setting, where all trees are of one species and close together, infections can be lethal. This has occurred in Venezuelan Caribbean pine plantations. Epidemics of another fungus, Ceratocystis, have been reported from acacia plantations in Costa Rica (Gilbert and Hubbell, 1996) and in Eucalyptus plantations in Republic of the Congo and Brazil (Wingfield, et al., 2001). Oil palm plantations in Southeast Asia carved out of forests are apparently responsible for the spread of a root-rot fungus, Ganoderma. In Australia, the incidence of and mortality from Armillaria, a pathogen of Eucalyptus trees, was greatly increased by selective logging, because of the exposure of living trees to freshly-cut (infected) stumps (Gilbert and Hubbell, 1996). Here, too, logging and other stresses incident upon logging increased the severity of infection of another root-rot fungus, Phytophthora cinnamoni, by increasing soil temperatures and moisture. This pathogen has reduced tree density in diseased areas by as much as 43% within 10 years, while at the same time, tree density increased 10% in uninfected areas. In diseased areas, the forest has become filled with large gaps and grassy areas. Healthy areas still retain an open canopy/woody understory structure. Forests may not recover from these insults for centuries, and epidemics may substantially alter the species composition of forests by removing many individuals of the susceptible species from the area of infestation (above data from Lodge, et al., 1996; for a discussion of plant diseases in tropical forests, see also Gilbert and Hubbell, 1996).

Logging also disturbs mosquitoes in the canopy, particularly malarial mosquitoes, and forces them to migrate from their normal forest environment – often to inhabited areas. Brazil now has the highest number of new cases of malaria in the world every year. In addition, new migrants into forests often introduce diseases to indigenous populations, and may carry local diseases back to urban areas. Many monkeys in the Cameroon rainforest are infected with immunodeficiency viruses similar to HIV and it is possible that these viruses may be transferred to humans when the monkeys are killed for food (Stephenson, 2002).