Concordance of HPV between vagina and cervix may be influenced by sample taking and by differences in flow of cervical epithelial cells. To investigate the latter aspect, from 96 women visiting their general practitioner, and 63 sex workers visiting a STI clinic, both vaginal and cervical samples for HPV detection were obtained by the doctor to standardize sample taking. To identify factors that may influence the flow of cervical epithelial cells to the vagina, a questionnaire on intimate hygiene was obtained. The overall HPV prevalence was 22.8%; 14.3% in the general population (14.3% in the cervix, 11.9% in the vagina), compared with 34.4% in sex workers (31.1% in the cervix, 27.9% in the vagina). There was excellent agreement between HPV prevalence in vaginal and cervical samples. The overall agreement was 94.5% (kappa = 0.83, 95% CI: 0.77-0.89); in the general population agreement reached 97.6%, compared with 90.0% in sex workers. Vaginal infection may influence concordance, but for validation of this finding larger studies are necessary. The high concordance found between HPV prevalence in vagina and cervix warrants further study of the applicability of self-sampling to improve coverage rates by attracting women who would otherwise not obtain a pap test.