Accumulating evidence indicates the potential correlation between the vaginal microbioma and the acquisition and persistence of Human Papillomavirus (HPV) infection. This study has as intention to demonstrate the potential relationship through a systematic review of the current literature. A search was conducted on the following medical databases: PubMed and Scopus. Nineteen studies were meeting our inclusion criteria and, finally, incorporated, in the present review. A total of 12,204 patients and their demographic characteristics were studied. Commercially available DNA tests and PCR were used for the detection of different HPV subtypes, while the identification of the microbiomes was performed through specific diagnostic methods and PCR assay. The most frequently encountered species were classified based on their protective or detrimental impact on the progression of HPV infection. The beneficial role of some types of Lactobacillus (Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus crispatus) is generally supported. On the other hand, high microbial diversity and specific microorganisms such as Sneathia, Anaerococcus tetradius, Peptostreptococcus, Fusobacterium and Gardnerella vaginalis were found to be implicated with higher frequency and severity of disease, potentially resulting in pre-cancerous and cancerous cervical lesions. The role of vaginal microbiota seems to play a -yet not fully understood- role concerning the susceptibility to HPV infection and its natural history.