The aim of the study was to investigate gene expression profiles of post-menopausal women receiving Premarin estrogen replacement therapy (ERT), compared to controls, and to examine any correlations between the bacterial vaginosis (BV) status of the subjects. Based upon an expected finding of a 50e60% difference between gene expression of host antimicrobials with alpha ¼ 0.05 (2-sided), beta ¼ 0.20 the calculation of 7 subjects per group, led to a sample size of 10 subjects receiving Premarin estrogen replacement therapy and 10 healthy, age-matched controls. Vaginal samples were collected at a single timepoint and processed for RNA recovery and Affymetrix array analysis, as well as Nugent scoring and denaturing gradient gel electrophoresis to identify bacteria. Lactobacillus iners was the most commonly detected species in the normal flora and this was confirmed with L. iners-specific PCR method. Vaginal swabs from 6 Premarin and 8 control vaginal samples provided a non-invasive means to analyze human gene expression. There was no significant up-regulation of cancer-associated gene expression in subject receiving Premarin ERT, but some evidence that the potentially protective innate immunity was reduced in patients with BV. Of those with a normal flora, there was a 2-fold down-regulation of carcinoma associated forkhead box A1 gene expression. BV was associated with 7-fold down-regulation of host antimicrobial colony stimulating factor, 9.83-fold for IL-1a, 8.33 for IL-1b and 3.63 for IL-6. This is the first study to use gene arrays to correlate changes in host expression response to estrogen replacement therapy and BV.