Since the first reported case of HIV infection in 1981, many HIV-seropositive patients have died as a result of diarrhoea induced by opportunistic protozoal infections: pathogens that would normally cause only a transient illness in immunocompetent individuals. The introduction of highly active antiretroviral therapy (HAART) in 1996 has been associated with a significant decline in incidence and mortality arising from infections such as cryptosporidia and microsporidia. Previously, there were no chemotherapeutic agents known to be effective in eradicating these parasites, but since the availability of HAART, the memory of the emaciated terminally ill patient with advanced AIDS suffering from refractory diarrhoea will hopefully be a thing of the past. Significant advances in the knowledge of the pathogenesis of HIV disease, earlier detection and thus treatment of the virus, and availability of improved diagnostic techniques and HAART have transformed the way HIV-associated diarrhoea is managed. In this review, we look specifically at the management of protozoa-induced diarrhoea.