Introduction: HIV infection and parasitic diseases constitute an important public health problem in many sub-Saharan African countries. The aim of this study was to assess the relationships between intestinal parasites, HIV/AIDS infection and Highly Active Antiretroviral Therapy (HAART). Methods: 332 HIV infected patients and 315 controls were recruited in a cross-sectional study. Stool and blood were collected from each participant. Stool specimen was examined in search of intestinal parasites by microscopy and blood sample was screened for HIV 1 and 2 antibodies. Results: The infection rates of intestinal parasites were higher in patients infected with HIV (19.9%; 66/332) than in those without HIV infection (11.7%, 37/315) (P=0.005). We have identified a total of eleven species of parasites in stool specimens: Entamoeba histolytica (6.0%), Blastocytis hominis (5.9%), Entamoeba coli (4.9%), Trichuris trichiura (1.2%), Ascaris lumbricoides (0.8%), Giardia intestinalis (0.8%), Strongyloides stercoralis (0.6%), Cryptosporidium parvum (0.6%), Isospora belli (0.5%), Microsporidia (0.5%) and chistosoma mansoni (0.1%). Infection with Cryptosporidium parvum, Isospora belli, and Microsporidia sp were found only among HIV positive patients. HAART was associated with a decrease of the rate of intestinal parasitic infection. Isospora belli and Microsporidia sp were diagnosed only in patients with CD4 cells counts <200 μL. Conclusion: The frequency of intestinal parasitic infestation was the highest among HIV positive patients. The absence of HAART increases intestinal parasitism. Cryptosporidium parvum, Isospora belli and Microsporidia sp were confirmed to be specific to people living with HIV/AIDS.