The pathophysiology of diseases produced by protozoal infections is caused not only by a direct effect of the parasites on their host (e.g. host cell lysis or parasite adherence), but also by indirect effects, where molecules of parasite origin exert an effect on host cells, which in turn produces a cascade of events (including the secretion of inflammatory cytokines, prostaglandins and nitric oxide) responsible for the symptomatology observed. The role of the host itself in the pathogenic events is not negligeable and its genetic background, nutritional and immunological status will influence the outcome of the infection (which will result in asymptomatic infections in some individuals and severe disease in others). The general and specific features of a variety of protozoal infections of medical and veterinary importance (including malaria, babesiosis, trypanosomiasis, toxoplasmosis, cryptosporidiosis, amoebiasis, giardiasis and trichomoniasis) are discussed in this review and a number of common patterns are identified.