Deforestation, fragmentation and habitat disturbance may alter the relationship between pathogens and hosts. We tested, apparently for the first time, whether habitat fragmentation and degree of dependence on forests affect the prevalence of avian blood parasites. We estimated the prevalence of Plasmodium, Haemoproteus and Trypanosoma through the inspection of 925 blood smears from 109 species captured in six pairs of small (< 30 ha) and large (> 1,000 ha) Brazilian Atlantic Forest fragments. Prevalence of the three types of parasites did not differ between small and large forest patches. Forest-independent birds were usually more infected with Plasmodium and Haemoproteus than other birds, but forest-dependent birds were more infected with Trypanosoma. Parasite richness on birds was not affected by patch size.