Protozoa infections are an important cause of chronic diarrhea in patients infected with HIV. The introduction of highly active antiretroviral treatment to the management of HIV in the mid 1990s has led to a dramatic reduction in the incidence of these opportunistic infections in Europe and America. In contrast, in the developing world where such treatments are not readily affordable, protozoa-related diarrhea remains a major cause of morbidity and mortality in HIV-infected individuals. In this review, the optimum investigations required to diagnose these pathogens in HIV-related diarrhea, as well as current treatment options, will be discussed.