Background: effectiveness of human papillomavirus (HPV) vaccines in the context of both guidelines which recommend vaccination at 14 years and modest vaccine coverage is poorly documented. Method: residual specimens from females aged under 25 years undergoing chlamydia testing were collected, together with demographic, sexual behaviour and vaccine status data. HPV genotypes were determined using the PapilloCheck® test system. We compared vaccine type (VT, types 6,11,16,18) prevalence according to vaccination status and identified factors associated with VT prevalence. Results: of 3736 eligible samples, 822 were from vaccinated women according to immunisation record, 1021 from women self-reporting vaccination and 1893 from unvaccinated women. Adjusted vaccine effectiveness for confirmed vaccinated compared with unvaccinated women was 95.93% (95%CI,90.22-98.32) against VT HPV and 38.37% (95%CI,12.68-56.51) against cross reactive genotypes (HPV31,33,45), respectively. VT HPV prevalence was significantly lower (.61%) among confirmed-vaccinated than among those who self-reported vaccination or unvaccinated women (1.76% and 15.0%, respectively). Factors associated with prevalent VT in multivariable analysis were vaccine status, positive C. trachomatis and e4 partners in the preceding year. Conclusion: our study demonstrates evidence of high effectiveness of HPV prophylactic vaccines at an individual level, supporting that wider implementation will help to reduce cervical cancer and precursors incidence.