OBJECTIVE: This study aimed to evaluate the human papillomavirus (HPV) vaccination status among a representative sample of young adults (YAs) with a special focus on the catch-up vaccination uptake among the male population in Switzerland. DESIGN AND SETTING: Data were extracted from an online self-administered questionnaire survey, conducted as a representative cross-sectional study in 2017. To understand correlations between vaccination uptake and sociodemographic characteristics, sexual health, and sexual behaviour, we performed bivariate analysis and multivariate regression analysis. PARTICIPANTS: Out of a total of 7142 participants, 2155 female and 996 male cisgender participants remained for statistical evaluation after excluding homosexual/bisexual study participants, those with gender dysphoria or those without knowledge of their vaccination status. OUTCOMES: The primary outcome of this study was to investigate HPV vaccination rates among female and male YAs in Switzerland. As secondary outcomes, we assessed uptake of catch-up vaccination and identified key factors influencing HPV vaccination uptake. RESULTS: Vaccination rates were significantly higher in the female group (40.9%), while not wanting to be vaccinated and doubting benefits and necessity of the vaccine were main reasons for non-vaccination. Vaccination coverage among male YAs was very low (7.8%), primarily due to insufficient information. Parents not being Swiss-born, a higher family socioeconomic status and having had a gynaecological visit at a younger age correlated with HPV vaccination uptake for female YAs. In the male group, participants with a higher number of lifetime partners and a younger age at first steady partnership were more likely to report a positive vaccination status. Knowledge about the benefits of catch-up vaccination was very limited among both genders. CONCLUSIONS: The lack of knowledge about benefits of HPV vaccination contributes to low vaccine uptake, especially occurring among the male population, must be addressed. Given the number of people who reported not knowing whether they were vaccinated or not, it is crucial to ensure that there is a thorough discussion about HPV and the protection the vaccine provides when presenting for vaccination.