Nowadays the right to conscientious objection triggers a wide spectrum of debates that lead to conflicting views with very strong arguments from both sides. Although in the past the right to conscientious objection was associated with military service, today in Republic of Croatia it is mostly mentioned in the context of medicine. Conscientious objection in medicine is a principle that entails some conflicting statements, but at the same time is the very needed principle which enables an individual to act in accordance with his or her moral and religious beliefs. The right to conscientious objection is based on the right to freedom of thought, conscience and religion which is guaranteed by numerous international conventions and by the Constitution of Republic of Croatia. The fundamental legal act, the Constitution of Republic of Croatia, in article 38, paragraph 1, guarantees the freedom of thought, conscience and religion, but in the doctrine, as well as in medical codes of ethics and deontology, we find the basis to restrict the mentioned freedom because conscientious objection is not an absolute right, it can be limited by legislative law. In this paper, the institute of conscientious objection in medicine, its essential elements and the definition itself, are the main topics that will be examined. This paper will also point out the legal sources that regulate it, its application in real life, especially in the context of reproductive medicine and the right to abortion on demand. In the end, the paper will offer some potential solutions to the problems related to already mentioned institute.