Background: In the Netherlands, human papillomavirus (HPV) vaccination is part of a national program equally accessible for all girls invited for vaccination. To assess possible inequalities in vaccine uptake, we investigated differences between vaccinated and unvaccinated girls with regard to various characteristics, including education and ethnicity, (both associated with non-attendance to the national cervical screening program), sexual behaviour and knowledge of HPV. Methods: In 2010, 19,939 nationwide randomly-selected 16-17 year-old girls (2009 vaccination campaign) were invited to fill out an online questionnaire. A knowledge scale score and multivariable analyses identified variables associated with vaccination status. Results: 2989 (15%) of the selected girls participated (65% vaccinated, 35% unvaccinated). The participants were comparable with regard to education, ethnicity, most sexual risk behaviour and had similar knowledge scores on HPV transmission and vaccination. However, unvaccinated girls lived in more urbanised areas and were more likely to have a religious background. Irrespective of vaccination status, 81% of the girls were aware of the causal relationship between HPV and cervical cancer, but the awareness of the necessity of cervical screening despite being vaccinated was limited. Conclusions: HPV vaccine uptake was not associated with knowledge of HPV and with factors that are known to be associated with non-attendance to the cervical cancer screening program in the Netherlands. Furthermore, most sexual behaviour was not related to vaccination status meaning that teenage unvaccinated girls were not at a disproportionally higher risk of being exposed to HPV. Routine HPV vaccination may reduce the social inequity of prevention of cervical cancer.