Abstract Although HPV vaccines are highly efficacious, a notable proportion of quadrivalent vaccinees are HPV18 seronegative post-vaccination. We have investigated this findings’ validity by comparing vaccine-induced antibody responses using two different immunoassays. 6558 16–17-year-old females participated in the FUTURE II (NCT00092534) and PATRICIA (NCT00122681) trials in 2002–2004. Both the quadrivalent and bivalent vaccine recipients (QVR and BVR) received three doses. Twelve-year follow-up for 648 vaccinees was conducted by the Finnish Maternity Cohort. The presence of neutralising and binding HPV antibodies was analysed via HPV pseudovirion-based neutralisation and pseudovirion-binding assays. Four percent and 14.3% of the QVRs were seronegative for neutralising and binding antibodies to HPV16 and HPV18, respectively. No BVRs were HPV16/18 seronegative post-vaccination. The antibody titres were strongly correlated between the assays, Pearson’s correlation coefficient, r [HPV16] = 0.92 and 0.85, and r [HPV18] = 0.91 and 0.86 among the QVRs and BVRs respectively. Fourteen percent of QVRs lacked detectable HPV18 antibodies in long-term follow-up.