BackgroundTo evaluate the HPV vaccination coverage in Boa Vista, Roraima (Brazil) and to identify personal and socioeconomic factors related to non-compliance to HPV vaccination.MethodsA school-based, cross-sectional study was conducted by distributing a self-administered questionnaire to the parents or guardians of pre-adolescent girls. The questionnaire addressed compliance to, knowledge about and perception of HPV and the HPV vaccine. Between July and November 2015, 13 private and public schools were visited based on a random cluster sampling method.ResultsA total of 1337 questionnaires were distributed to all female students in the target age group, and 797 were completed and returned (the participation rate was 59.6 %). The vaccination coverage rate was 82.7 % and was higher among public school students than among private school students (84.1 % vs 56.3 %; p = 0.003). Most parents (60 %) incorrectly answered more than half of the questions related to HPV knowledge, and limited knowledge about HPV and the HPV vaccine correlated with lower compliance to vaccination (adjusted OR = 1.42; 95 % CI: 1.01 to 2.76). In the perception analysis, the belief that the HPV vaccine is important for the daughter was an important protective factor (adjusted OR = 0.62; 95 % CI: 0.23 to 0.93), and concern about adverse effects of the HPV vaccine was a risk factor for non-compliance (adjusted OR = 1.66; 95 % CI: 1.01 to 2.71). Family income, religion and education level of the parents or guardians did not correlate with compliance to vaccination.ConclusionHPV vaccination coverage was high in Boa Vista, Brazil, but knowledge about the vaccine was deficient. This deficiency was associated with a distorted perception and was negatively associated with compliance to vaccination. Actions aimed at informing the public about the HPV vaccine, including its risks and benefits, are needed to attain higher vaccination coverage in Brazil.Electronic supplementary materialThe online version of this article (doi:10.1186/s12913-016-1677-y) contains supplementary material, which is available to authorized users.