BACKGROUND Prevalence of intestinal parasitic infections in HIV-positive people and its association with clinical and socioeconomic factors has been investigated on the mainland of Equatorial Guinea, in order to define the precise measures for improvement of their quality of life. METHODS In August 2010, 273 HIV-positive and 60 HIV-negative were recruited. A sample of faeces, T-CD4+ cell counts, and clinical, socioeconomic and demographic data were collected from each patient. Stool samples were analysed by microscopy and immunochromatography. Data were analysed by Pearson's χ2 test and the risk of each factor was measured by odds ratio bivariate analysis. RESULTS Two hundred and ten (76.9%) HIV-positive participants were infected by intestinal parasites and 16 parasite species were identified; 246 (48.9%) were pathogenic helminths, 159 (22.9%) pathogenic protozoa and 142 (28.2%) opportunistic protozoa. Trichuris trichiura, Entamoeba histolytica/dispar/moshkovskii, Ascaris lumbricoides and Giardia duodenalis were the most prevalent parasites; 52 (86.7%) of HIV-negative participants were parasitized. HIV was related to co-infection by Entamoeba spp., E. nana and Blastocystis hominis. CONCLUSIONS The high rates of parasitic infections found highlights the urgent need of environmental sanitation, health education and water distribution actions, as well as early diagnosis and treatment of intestinal parasites.