[[Image:Stefanos of Tallinn.jpg|125px|right|thumb|Metr. [[Stephanos (Charalambides) of Tallinn|Stephanos (Charalambides)]]]]
An agreement was reached in which local congregations could choose which jurisdiction to follow. The Orthodox community in Estonia, which accounts for about 14% of the total population, remains divided, with the majority of faithful (mostly Russians) remaining under Moscow. As of a government report of November 2003, about 20,000 believers (mostly Estonians) in 60 parishes are part of the autonomous church, with 150,000 faithful in 31 parishes, along with the monastic community of Pukhitsa, paying allegiance to Moscow.
In 1999, the church gained a resident hierarch (it had been under the Archbishop of [[Church of Finland|Finland]] as ''[[locum tenens]]''), Metropolitan [[Stephanos (Charalambides) of Tallinn|Stephanos (Charalambides)]], who had formerly been an [[auxiliary bishop]] under the Ecumenical Patriarchate's Metropolitan of France.