Abstract Objectives: A study was conducted to use new molecular technologies to identify the vaginal bacterial species of postmenopausal women under oral estrogen therapy (Premarin-conjugated equine estrogen, CEE). Study design: Nineteen postmenopausal women under CEE treatment were recruited and their vaginal flora were analyzed during 3 months, using polymerase chain reaction in combination with denaturing gradient gel electrophoresis (DGGE) and sequencing of DNA fragments. Results: Sixty-eight percent of the women presented with a ‘Normal’ Nugent score at the first sampling time (d0). All the subjects had bacterial species detected in their vaginal flora. Lactobacillus species were detected in all samples. Moreover, 53% of the women had lactobacilli exclusively at d0. Two Lactobacillus species were dominant, and were recovered from the majority of samples ( L. iners and L. crispatus). Forty-four percent of the samples also contained other bacterial species, which were potential urogenital pathogens. Candida albicans was detected in 26% of the subjects. The vaginal flora of the women under CEE treatment were different from that of postmenopausal women not receiving hormone therapy, but very similar to premenopausal women. Conclusions: The present study indicates that one benefit from hormone replacement therapy (HRT) is the restoration of a lactobacilli vaginal flora associated with a protective effect against urogenital infections.