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Despite being a captive nation under the rule of the officially atheistic Soviet regime for nearly half of the 20th century, the Baltic country of Estonia (population 1.34 million) has historically been a Christian nation. Its first encounters with Christianity date to the 11th century, when Orthodox missionaries first appeared in the eastern areas closest to the present-day Russian state. However, it was the northern crusade of the 13th century, with the twin goals of territorial conquest and the conversion of Europe's last pagans, that brought Roman Catholicism to the Estonian lands. While German knights conquered the northeastern tribes, German priests baptized them and administered the faith during the later Middle Ages. In the 16th century, however, the region's rulers broke with the Church and embraced Lutheranism, which became the principal religious confession of both the German minority and the Estonian majority. While the Germans who dominated the region left Estonia (and neighboring Latvia) during World War II, the Russians, who began arriving in large numbers in the 19th century, supplanted the Germans as Estonia's principal minority and brought the Orthodox faith with them.

For half a century, religious life in Estonia was suppressed by the Soviet regime, whose arrival in 1940 to 1941 resulted in the arrest, exile, or outright murder of thousands of people whom the new authorities regarded with suspicion and hostility—including dozens of Lutheran pastors. Partly as a result of the Soviet regime's draconian policies, church membership declined in Estonia, which today is one of Europe's most secularized countries.

The Estonian state today has no official church, and the constitution provides for full freedom of religion; yet only 30% of the Estonian population profess any religious faith at all. The main profession of the country's ethnic Estonians (who constitute nearly 70% of the population today) is the Estonian Evangelical Lutheran Church, with an estimated 180,000 members (less than 13% of the total population).

While most ethnic Estonian believers are affiliated with the Lutheran Church, most of the country's ethnic Russians, constituting about a quarter of the population, are Orthodox. In Estonia, Orthodoxy been divided since 1944, when the leaders of the autocephalous Estonian Apostolic Orthodox Church (EAOC), which was canonically subordinate to the Patriarchate of Constantinople, fled Estonia and settled in Sweden. Meanwhile, Orthodoxy in Soviet-occupied Estonia came under the control of the Moscow Patriarchate. With the restoration of Estonian independence in 1991, a struggle between the EAOC and the Diocese of the Moscow Patriarchate immediately ensued, with each claiming to be the legal successor to the prewar Estonian Orthodox Church and, thus, the legal inheritor of its property. While the Moscowbased church, now registered as the Estonian Orthodox Church of the Moscow Patriarchate, ended up being the loser of the struggle, there can be little doubt that the Russian-language Orthodox congregations are stronger and more influential than the Estonian congregations of the EAOC.

Among the other religious groups in Estonia are a small Jewish community of about 2,500 people, residing mostly in Tallinn, as well as communities of Old Believers (an Orthodox splinter whose adherents fled to Estonia to escape tsarist persecution), Catholics, Baptists, Methodists, and other religious associations. American evangelical religious influence is felt in Estonia in the form of its small communities of Pentecostals and Jehovah's Witnesses.

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