We investigated the effects of bacterial vaginosis (BV) on the outcomes of high-risk human papillomavirus infection (HR-HPV). BV was diagnosed on Papanicolaou-stained cytology slides of 707 HPV-positive patients. HR-HPV DNA expression was analysed using the Hybrid Capture II (HC-II) assay. Of the 707 HR-HPV-positive female patients, 298 (42.1%) exhibited clearance of HR-HPV. The remaining 409 patients had persistent HR-HPV infection. The persistent HR-HPV group and the clearing group had similar rates of BV at the beginning of the study. At the end of the study, the persistent HR-HPV group had a BV prevalence of 11.2% while the clearing group had a significant lower BV prevalence of 5.0%. A decreased clearance of HPV was found in women with current BV, compared with women without BV. Furthermore, the natural history of HPV was not affected by the HPV viral load or the BV prevalence at the beginning of the study (P > 0.05). Bacterial vaginosis appears conducive to the persistence of HPV infection.