Abstract: The vaginal swabs among HIV-positive women in Africa often revealed opportunistic infections such as human Papillomavirus (HPV) and Mycoplasma that induce respectively cervix cancer and diseases such as vaginosis, abortions, infertility in through salpingitis. The purposes of this study were to: (1) seek for, the prevalence of pathogens such as HPV and Mycoplasma; (2) characterize the strains of HPV and estimate their prevalence; (3) identify among these women, those who were co-infected by these pathogens in order to cure them. From February 2009 to January 2010, 156 HIV-positive women attending our medical centers and aged from 19-45 years (mean age 33.65±5.75 years) had voluntarily accepted vaginal specimen’s tests. PCR, ELISA and molecular hybridization were used for the identification and characterization of these pathogens. The results revealed the presence of Mycoplasma and HPV in 25.64 and 58.33% cases, respectively. The following HPV genotypes and the following prevalence were recorded: HPV-50'S (24.11%), HPV-18 (21.28%), HPV-30'S (18.44%) and HPV-16 (5.67%). The study also enable the identification of co-infections such as HPV-18 strains with HPV-30'S (5.67%) and HPV-30'S with HPV-50'S (3.55%). Other germs infecting the female genital tract including Candida albicans (20.51%), Escherichia coli (12.18%), Treponema pallidum (3.85%), Streptococcus agalactiae (3.21%) and Staphylococcus aureus (1.92%) were isolated. This preliminary research work showed the incidence of several genital pathogens, this could be a springboard for nationwide epidemiological study on HPV strains circulating in Burkina Faso.