The female reproductive tract, similar to other mucosal sites, harbors a specific microbiome commonly dominated by Lactobacillus species (spp.), which has an essential role in maintaining health and homeostasis. Increasing evidence shows that genital tract dysbiosis and/or specific bacteria and cytokines might have an active role in the development and/or progression of HPV infection and cervical intra-epithelial neoplasia (CIN) and as a result cervical cancer. Cross-sectional and longitudinal studies reported that Lactobacillus spp. depletion increases with severity of CIN and that this may negatively affect disease regression rates. It is plausible that Lactobacillus deplete microbiome composition may lead to a pro-inflammatory environment that can increase malignant cell proliferation and HPV E6 and E7 oncogene expression. Future longitudinal cohorts and mechanistic experiments on HPV transfected cells models will further permit exploration of the impact of Lactobacillus spp. on HPV infection.