After adjusting for sex, age, and variables with p-values < 0.10 in the bivariate analysis (hospital, current CD4+ count < 200 cells/μL, viral load uncontrolled >20 copies/mL, daily diarrhea, homosexual practices, prior intestinal parasite infection, gonococcal infection and toxoplasmosis), homosexual practices (compared with heterosexual, bisexual, or transgender practices) were significantly associated with a higher risk of pathogenic protozoa positivity (p: 0.045; adjusted OR: 2.52; 95% CI: 1.04–6.12). This evidence concerns the gene CD4 and parasitic intestinal disorder.