<p>Declining vaccination rates and the overall rise in vaccine hesitancy have become significant health threats globally. Given the complexity of vaccine hesitancy, it is crucial to study the subjective beliefs and viewpoints of vaccine-hesitant individuals. Q methodology study was carried out with Estonians (<i>N</i> = 29) holding a range of vaccine-hesitant views, from strong anti-vaccine sentiments to expressing doubts about vaccines, to explore their subjective understandings and opinions on the topic of vaccines. As a result of our analysis, two factors emerged: “Mainstream Medicine Non-Trusting Vaccine Sceptic” (Factor 1) and “Mainstream Medicine Trusting Vaccine Hesitant” (Factor 2). Individuals loading onto Factor 1 held several views commonly associated with anti-vaccine rhetoric and conspiratorial thinking. Despite their profound interest in health topics, they showcased no trust in medical doctors and the mainstream medical system, preferring alternative medicine. During the COVID-19 pandemic, representatives of Factor 1 realised that their views about vaccines were not shared by the public, leading to feelings of exclusion. Individuals loading onto Factor 2 expressed high levels of trust in medical doctors and the medical system. They also exhibited prosocial concerns and believed in the importance of collective responsibility. They were very interested in the topic of vaccines and actively sought information from a wide range of channels, but inadequate public communication and overall polarisation during the COVID-19 pandemic only intensified their hesitancy. Both types of emerged types exhibited an individualist epistemology, attributing a central role to the individual in obtaining knowledge and deciding what is true. Such a stance reveals a need to establish long-term national educational programmes for developing citizens’ health literacy, as well as promoting non-judgemental, collaborative communication between vaccine-hesitant individuals and medical doctors, policymakers, and the media.</p>