The purpose of this study was to evaluate the prevalence of different microorganisms, and the influence of menstrual cycle, CD4+ cells and viral load in vaginal flora, and compare different diagnosis methods in asymptomatic Human immunodeficiency virus HIV- and HIV+ women. Variables like contraception methods, type of sexual intercourse, and menstrual cycle phase were significant between groups. The clinical evaluation of vaginal pH and type of discharge, besides intraepithelial lesions, do not seem to have influence in microflora . Fresh wet-mount microscopy and bacterioscopy demonstrated no difference. HIV+ presented predominance of Gardnerella, Candida, Trichomonas, and Mobiluncus in cervicovaginal cytology, and vaginal culture exhibited higher prevalence of Gram+ and coagulase-negative staphylococci. Fresh wet mount microscopy showed a sensitivity of 88.9%, and the bacterioscopy sensitivity was 75%. Clinical exam specificities were 76.3% and 94.9%, respectively. Asymptomatic HIV+ women may present diversified vaginal microenvironment, possibly making them more prone to pelvic inflammatory disease, sexually transmitted infection (STI), and infertility.