Habitat fragmentation and deforestation are thought to disrupt host–parasite interactions and increase the risk of epizootic outbreaks in wild vertebrates. A total of 220 individuals from three species of African rain-forest bird (Andropadus latirostris, Andropadus virens, Cyanomitra obscura), captured in two pristine and two agroforests in Cameroon, were screened for the presence of avian haemosporidian parasites (species of Plasmodium and Haemoproteus) to test whether habitat differences were associated with differences in the prevalence of infectious diseases in natural populations. Thirteen mitochondrial lineages, including 11 Plasmodium and two Haemoproteus lineages were identified. Whereas levels of Haemoproteus spp. infections were too low to permit analysis, the prevalence of infections with Plasmodium spp. reached significantly greater levels in undisturbed mature forests. Importantly however, the significant association between forest type and parasite prevalence was independent of host density effects, suggesting that the association did not reflect changes in host species composition and abundance between forest types. Our results illustrate how characterizing land-cover differences, and hence changes, may be a prerequisite to understanding and predicting patterns of parasite infections in natural populations of rain-forest birds.