Introduction: The objective of this work was to assess the prevalence of bacterial vaginosis (BV) and genital mycoplasma colonization in 251 HIV-positive compared to 200 HIV-negative women at the Maternal and Child Health (MCH) service of Saint Camille Medical Center Ouagadougou (Burkina Faso). Methodology: After revealing the cervix with a speculum, we collected swabs of vaginal discharge for the detection of pathogenic bacteria. Results: Among HIV-positive and HIV-negative women, we identified respectively: Mycoplasma hominis (16.7% versus 5.5%); Ureaplasma urealyticum (16.3% versus 0.0%); co-infection M. hominis with U. urealyticum (13.14% versus 0.0%); Candida albicans (21.11% versus 41.5%); E. coli (9.96% versus 4.0%); and the presence of abundant vaginal discharge (27.5% versus 5.0%) respectively. The Nugent's score, utilized for the diagnosis of BV, was significantly higher in HIV-positive women (p < 0.001) associated with poor vaginal hygiene practices (p < 0.01) and no use of condoms (p < 0.01). Enterobacter, Klebsiella pneumonia, Klebsiella oxitocica, Staphylococcus epidermidis and Staphylococcus aureus, Streptococcus agalactiae, Trichomonas vaginalis, and Gardnerella vaginalis were also isolated, but in a low prevalence ranging from 0% to 5%. Conclusion: These results demonstrate that the HIV-positive women of Burkina Faso are frequently affected by BV and represent a reservoir for mycoplasma infection. Since these germs can lead to sterility and premature delivery, it is important to develop a policy of screening.