BackgroundHPV vaccination decision-making is a complex process that is influenced by multiple psychosocial determinants. Given the change in policy recommendation to include males in routine HPV vaccination, our goals were to assess the HPV vaccination uptake in Canada, to understand where Canadian parents were situated in the HPV vaccine decision-making process for their son, how they changed over time and which psychosocial determinants were relevant for this process.MethodsWe used an online survey methodology and collected data from a nationally representative sample of Canadian parents of boys aged 9–16 at baseline (T1, February 2014) and at 9 months’ follow-up (T2). Our analyses were guided by the Precaution Adoption Process Model (PAPM), a theoretical health behavior model that classifies parents in one of six stages: unaware, unengaged, undecided, decided not to vaccinate, decided to vaccinate and those who had already vaccinated their sons. Rigorous methods were used to filter out careless responders: response variance, bogus items, psychometric antonyms and psychometric synonyms.ResultsAt T1 and T2, we received 3,784 and 1,608 respectively completed questionnaires; after data cleaning 3,117 (T1) and 1,427 (T2) were retained. Less than 3% of boys were vaccinated at both time points. At both T1 and T2, most parents (over 70%) belonged to the earlier vaccination adoption stages: 57% were unaware (T1) and 15.3% (T2); 20.9% were unengaged (T1) and 32.4% (T2); and 9.1% were undecided (T1) and 25.2% (T2). At follow-up, 37.7% of participants did not move from their initial PAPM decision-making stage. Most parents (55%) preferred to receive information from their healthcare provider (HCP) but only 6% (T1) and 12% (T2) had actually spoken with a HCP about the HPV vaccine for their son.ConclusionsHPV vaccination uptake in Canadian boys was very low in the absence of a publicly funded HPV vaccination programs for boys. Optimal HPV information preferences were identified and can be used in interventions to increase HPV knowledge and increase HPV vaccine uptake. Intentions to vaccinate or planning to speak to one’s HCP did not translate into action for most parents over the 9-month follow up; this finding is critical to consider to inform implementation strategies. Methodological challenges are described and suggestions for future research are offered.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-016-3828-9) contains supplementary material, which is available to authorized users.