In this paper, the authors analyse the impact and role of the principle of proportionality in the field of compulsory vaccination as a possible limitation of certain convention rights sui generis. In particular, this is observed in the light of the rights protected by Articles 6 and 8 of the European Convention for the Protection of Human Rights and Fundamental Freedoms. The starting point of the research is the claim of the European Court of Human Rights in the case of Sanofi Pasteur v. France that "it was necessary to weigh between two aspects of the protected right to a fair trial - the right of access to court and (the principles) of legal certainty and determine which one to give priority to." In this light, the "moderation" of the principle of proportionality and the margin of appreciation of states is observed with regard to the indicated aspects of the right to a fair trial in civil matters and the convention protection granted. On the other hand, in the case Vavrička and others v Czech Republic, the introduction of measures of compulsory vaccination of children is observed in the context of Article 8 of the Convention and it directs the answer to the question of the necessity and proportionality of restriction, also in the context of margin of appreciation, in order to answer whether or not it violates a protected right. The principle of proportionality helps to achieve a 'fair balance' between conflicting convention rights (or two conflicting aspects of an individual right) on the one hand, and between convention law and general or public interests, on the other. Therefore, the application of that principle is also evident in the above mentioned cases in which the Court examined the 'conflict' between two aspects of the right to a fair trial, the right of access to court and legal certainty, as well as the 'conflict' between the right to respect for private and family life and the protection of the health and rights of others. One of the elements for assessing the proportionality of restrictions is the "adequacy" of the civil law system of damages, which should be examined under national law. By exploring the influence and role of the margin of appreciation as another aspect of the principle of proportionality, in light of the conclusions drawn from these cases, it is evident that the breadth of its permissible limits varies and depends on various factors such as the nature of the relevant convention law, the importance of the right of the individual, the extent and strength of interference, and the nature of the objective of the restriction. Following this, one of the relevant questions is whether the application of the principles of proportionality and of the margin of appreciation differs in the above mentioned cases. In the context of these cases, the most recent decision of the European Court against Croatia (J.Č. v. Croatia) will be mentioned in light of the previous decision of the Constitutional Court (U-III-7725/2014), in which the European Court examined the national framework and existing case law regarding compulsory vaccination of children. Another dimension to the research is provided by an overview of different options for insuring against the risks of vaccination consequences, ranging from product liability insurance to life insurance and accident insurance.