Parasitic infections responsible for diarrhea have a worldwide distribution, overlapping with AIDS in most countries. Indeed, highly active antiretroviral therapy has markedly reduced the incidence of most parasitic opportunistic infections, but parasite-related diarrhea remains frequent and probably underestimated in developing countries. In this review, we focus on the advances in molecular epidemiology, diagnosis and current treatment of the most prevalent parasitic infections in HIV-infected patients. Most of these parasites are protozoa, whose diagnosis at the laboratory requires some adapted technique and expertise. We highlight the importance of diagnosis and the skill of the laboratory of parasitology, since most parasitic infections responsible for diarrhea in AIDS patients can be treated.