Background Recent hepatitis A virus outbreaks in Europe affecting men who have sex with men (MSM) and ongoing hepatitis B virus transmission among MSM underscore the ongoing need for viral hepatitis prevention in this population. Aim To describe viral hepatitis knowledge and associated factors among MSM in the WHO European Region to inform targeted prevention. Methods In the European MSM Internet Survey (EMIS-2017), basic knowledge was defined as correctly identifying at least 4 of 5 statements about viral hepatitis and vaccination. We described basic knowledge by country. In a multilevel logistic regression model, we estimated adjusted odds ratios (aOR) with 95% confidence intervals (CI) for having basic knowledge and explanatory variables: sociodemographic characteristics, history of hepatitis C and/or HIV diagnosis, sexual orientation disclosure at last sexually transmitted infections (STI) test and outness. Results Of 113,884 participants across 43 WHO European Region countries, 68% demonstrated basic knowledge, ranging from 50% in Israel to 80% in the Netherlands. Basic knowledge was significantly associated with older age (≥ 40 years vs < 25 years, aOR: 2.9, 95% CI: 2.7–3.0), a history of hepatitis C and/or HIV diagnosis (aOR: 1.8, 95% CI: 1.7–1.9) and sexual orientation disclosure at last STI test (aOR: 1.3, 95% CI: 1.2–1.3), among other factors. Conclusions We found a knowledge disparity regarding viral hepatitis and hepatitis vaccination awareness among MSM across Europe, highlighting a need to address these gaps. A non-judgemental, accepting climate that allows individuals attending medical services to safely disclose their sexual orientation is fundamental to enable healthcare professionals to target information and preventative measures more effectively.