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On April 15, 1950, he was [[ordination|ordained]] a [[deacon]] by Metropolitan Gregory (Chukov) of Leningrad, and on April 17, 1950, he was ordained a [[priest]] and appointed [[rector]] of the [[Theophany]] church in city of [[w:Johvi|Johvi]], Estonia, in the Tallinn Diocese. On July 15, 1957, Fr. Alexei was appointed Rector of the Cathedral of the [[Dormition]] in Tallinn and [[Dean]] of the [[W:Tartu|Tartu]] district. He was elevation elevated to the rank of Archpriest on August 17, 1958, and on March 30, 1959, he was appointed Dean of the united Tartu-[[W:Viljandi|Viljandi]] deanery of the Tallinn diocese. On March 3, 1961, he was [[tonsure]]d a [[monk]] in the Trinity Cathedral of [[Holy Trinity-St. Sergius Lavra]].<ref name="official bio" />

Since the collapse of the Soviet Union there have been accusations that Patriarch Alexei had ties to the KGB, which resulted from documents which allegedly came from the KGB's archives in Estonia, and which refer to Patriarch Alexei with the code name "Drozdov."<ref>See for example, ''The Wall Street Journal'', [http://online.wsj.com/article_email/SB118469533202469128-lMyQjAxMDE3ODE0NzYxOTc1Wj.html 'Cold War Lingers At Russian Church In New Jersey'] December 28, 2007.</ref> It should be noted that it was very unusual for any person to be referenced in KGB documents prior to 1980 without a similar code name, regardless of an affiliation with the KGB. Patriarch Alexei has always denied that he was a KGB agent,<ref>"Official spokesman for the Moscow Patriarchy Father Vsevolod Chaplin labeled such reports as 'absolutely unsubstantiated' in a Wednesday interview with Interfax. 'There is no data indicating that Patriarch Alexy II was an associate of the special services, and no classified documents bear his signature,' he said. 'I do not think that direct dialogue between the current patriarch and KGB took place,' Father Vsevolod continued. However, 'all bishops communicated with representatives of the council for religious matters in the Soviet government, which was inevitable, since any issue, even the most insignificant one, had to be resolved through this body. It is quite another matter that the council forwarded all its materials to the KGB,' he said." [http://www.stetson.edu/~psteeves/relnews/0009b.html Moscow Patriarchate Rejects Times Report of Alexy II'S Collaboration with KGB, Sept 20, 2000 (Interfax)]. "Chaplin, the church spokesman, said in March, 'Nobody has ever seen a single real document that would confirm the patriarch used his contacts with Soviet authorities to make harm to the church or to any people in the church.' " [http://www.stetson.edu/~psteeves/relnews/0205e.html Russia's Well-Connected Patriarch, ''Washington Post'' Foreign Service, 23 May 2002]; "Father Chaplin said: 'In recent times many anonymous photocopies of all sorts of pieces of paper have been circulated. In none of them is there the slightest evidence that the individuals we are talking about knew that these documents were being drawn up, or gave their consent. So I don't think any reasonably authoritative clerical or secular commission could see these papers as proof of anything.' " Russian Patriarch 'was KGB spy', ''The Guardian'' (London), February 12, 1999.</ref> and the authenticity of the documents in question have been disputed on the basis on the basis that they use anachronistic fonts which did not exist at the time the document ostensibly originated from, and that the Estonian government fabricated the documents in order to discredit the Russian Orthodox Church.<ref>Alexey Chumakov [https://listserv.indiana.edu/cgi-bin/wa-iub.exe?A2=ind0010A&L=ORTHODOX&P=R3102 Agent Drozdov?], December 28, 2007.</ref>