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Background: Depression of the immune system caused by the human immunodeficiency virus (HIV) promotes the onset of opportunistic infections including intestinal parasites. Objectives: In this study, we are comparing the prevalence of these parasitic infections among individuals infected with HIV (HIV+) and non-infected (HIV-) enrolled in four HIV care units in the Centre Region of Cameroon. Methods: A cross-sectional study was conducted and stool samples were collected from 283 HIV positive subjects and 245 seronegative subjects. These samples were processed using direct wet mount, formol-ether concentration, Kato-Katz procedure, modified Ziehl-Neelsen staining, and Baermann techniques to identify both common and opportunistic intestinal parasites. Logistic regression analyses were used to assess the association between HIV infection and socio-demographics factors as well as infection with intestinal parasites. Results: A total of 123 (23.4%) individuals were found infected with at least one protozoan parasite species, and nine (1.7%) with intestinal worms. Overall, infection rates were 27.9% and 22.4% among HIV+ and HIV- subjects, respectively. The frequencies of Cryptosporidium spp. and Entamoeba histolytica/dispar were significantly more important among HIV+ subjects (P < 0.0455). Pentatrichomonas hominis and Entamoeba coli were significantly more prevalent among HIV- subjects (P < 0.0210). Heterogeneity was observed in the distribution of intestinal parasites, according to socio-demographic parameters. In addition, Cryptosporidium spp. was significantly associated with the decrease in CD4 cell count (P = 0.0035). The frequencies of infections with Cryptosporidium spp., Isospora belli, and Iodamoeba buetschlii were significantly more important in HIV positive patients not taking antiretroviral (P < 0.0226). Conclusions: Cryptosporidium spp., Entamoeba histolytica/dispar, and Blastocystis spp. were the intestinal pathogens more often found among HIV infected individuals. HIV positive subjects were significantly more infected with intestinal parasites than seronegatives in intermediate and rural settings, among individuals aged more than 45 years and among unemployed individuals.