Although vaccination is recognised as the top public health achievement of the twentieth century, unequivocal consensus about its beneficence does not exist among the general population. In countries with well-established immunisation programmes, vaccines are “victims of their own success”, because low incidences of diseases now prevented with vaccines diminished the experience of their historical burdens. Increasing number of vaccine-hesitant people in recent years threatens, or even effectively disables, herd immunity levels of the population and results in outbreaks of previously already controlled diseases. We aimed to apply a framework for ethical analysis of vaccination in childhood based on the four principles of biomedical ethics (respect for autonomy, nonmaleficence, beneficence and justice) to provide a comprehensive and applicable model on how to address the ethical aspects of vaccination at both individual and societal levels. We suggest finding an “ethical equilibrium”, which means that the degree of respect for parents’ autonomy is not constant, but variable; it shall depend on the level of established herd immunity and it is specific for every society. When the moral obligation of individuals to contribute to herd immunity is not fulfilled, mandatory vaccination policies are ethically justified, because states bear responsibility to protect herd immunity as a common good.