More data are needed on the role of abnormal vaginal microbiota in the natural history of cervical human papillomavirus (HPV) infections. Our purpose was to study the prevalence of mixed flora (MF), bacterial vaginosis (BV) and yeast infection in women with known HPV outcomes during the 72-month follow-up (FU). Asymptomatic pregnant women (N = 329) were enrolled in the third trimester of their pregnancy. Pap smears and HPV genotyping samples were taken at baseline and at 12-, 24-, 36- and 72-month FU visits, with one additional sample at 2 months for HPV. HPV testing was done with nested PCR and Multimetrix assay to determine the point prevalence and persistence of HPV. Conventional Pap smears were scored for MF, BV and yeast infection. Covariates of the outcomes were analyzed using generalized estimating equation (GEE) and Poisson regression. Of the women, 76.6% (252/329) tested HPV-positive at least once during the FU. BV was detected in 12.2% (40/329), MF in 57.4% (189/329) and yeast infection in 22.9% (73/329) of the women. HPV-positive women had significantly more leucocytes in their Pap smear (p = 0.023) than the HPV-negative ones. MF (OR 2.75, 95% CI 1.77–4.27) and yeast infection (p = 0.007) were linked with HPV positivity. BV but not yeast infection was a significant covariate of HPV persistence (p = 0.024; OR 2.15, 95% CI 1.13–4.08). MF and yeast infection were associated with prevalent cervical HPV infection. In the longitudinal setting, BV predicted HPV persistence, implicating that treatment of asymptomatic BV in women with cervical HR-HPV infections might be justified.