Objective: To assess the prevalence of bacterial strains and fungal strains infecting the vaginal tract and test their sensitivity to antibiotics in women attending Saint Camille Medical Centre in Ouagadougou. Methods: From January 2008 to December 2009, a total of 2000 vaginal swabs were cultivated for bacterial and fungal identification and isolation. Furthermore, bacterial strains were tested for their susceptibility to several antibiotics used in routine in the centre.Results:1536/2000 sample, a positivity rate of 76.80%. Candida albicans (48.76%), followed by Escherichiacoli The results revealed that microbial isolation and identification was attempted for (16.67%), Streptococcus agalactiae (8.14%) and Staphylococcus aureus (7.55%) were the major agents of genital tract infections in patients. Mycoplasma hominis and Ureaplasma urealyticum combined accounted for less than 7%. Trichomonas vaginalis was identified in 1.04% cases. The antimicrobial tests revealed that the microorganisms developed resistance to several antibiotics including beta lactams. However, antibiotics such as cefamenzol, ciprofloxacin and norfloxacin were still active on these bacteria. Conclusions: The results reveal that many sexually active women are infected by one or more microbial pathogens, probably because of the lack of hygiene or the adoption of some risky behaviors, such as not using condoms or having multiple sexual partners. Efforts should be made to address these points in the country.