The paper aims to analyse several theoretical problems concerning the recognition of the right to conscientious objection to compulsory vaccination. Our interest in the matter has stemmed from our domestic experience in the Czech Republic, ie a country with a traditional, comprehensive system of compulsory vaccination, but also a country in which the Constitutional Court recognised that, under certain conditions, conscientious objections to compulsory vaccination may be successfully invoked. The Constitutional Court created a special four-prong test for public authorities to ascertain whether the conscientious objection is legitimate to the case at hand and compulsory vaccination should not be enforced. We believe that sharing the Czech experience and pinpointing its crucial, but also debatable, aspects (especially the legal basis for the recognition of conscientious objection and the test itself) may be a useful comparative material for other states with a system of compulsory vaccination, or states which contemplate its introduction, possibly even against Covid-19. However, to add a broader European perspective, the paper will also examine the context of the relationship between compulsory vaccination and conscientious objection in the light of the Convention and will analyse the relevant case-law of the Strasbourg Court. A definitive answer as to whether a conscientious objection to compulsory vaccination may entail the protection of Article 9 of the Convention has not yet been given by the Strasbourg Court. Nevertheless, we argue that the case-law indicates that, under certain conditions, conscientious objections could attract the guarantees of Article 9 in future cases.