The article is an analysis of legal and axiological source of conscientious objection. The study was based on the European and national system of human rights protection. Freedom of conscientious objection is recognized by both Article 9(1) of the European Convention on Human Rights and Article 10(2) of the Charter of Fundamental Rights of the European Union. The problem of conscientious objection is the subject of the analysis of the doctrine in connection with the judgment of the Polish Constitutional Tribunal of 7 October 2015 in case K 12/14, which concerned the doctor’s conscience clause. The conscientious objection protects the hard core of dignity and its essence. The human right to freedom of conscience and religion is one of the closest, if not the closest, to dignity of the human being. The author also points out the scope of the human right to conscientious objection and claims that it should have a subsidiary character, be limited to justified cases, as well as seek to protect the interests stipulated in the systems of natural law or positive law.