The predominant religion of indigenous ethnic Estonians has traditionally been Christianity, in the form of the Protestant Evangelical Lutheran confession; however, less than a quarter of ethnic Estonians define themselves as active believers at present. Most believers amongst the Russian minority are Eastern Orthodox. The Ecumenical Patriarchate of Constantinople has since the 1920s recognised a separate national Estonian Orthodox Church, which has led to strained relations with the Russian Orthodox Church, which claimed sole authority over Orthodox believers in the country during the period of Soviet rule.

Today, over 31% of the adult population are active followers of a particular faith, consisting of the following: 15% Estonian Evangelical Lutheran Church, 14% Orthodox,  0.5% Baptists, 0.5% Roman Catholics.

There is also a number of small Buddhist, Protestant and Jewish groups, and some neopagans who revere the local ancient deity Taara