Recently, Father Gleb and the Committee of Freedom of Conscience initiated legal action against Alexander Dvorkin, director of the Holy Martyr Irenaeus of Lyon, for libel after Dvorkin published a brochure accusing various minority faiths of having "criminal orientations" and practicing as "totalitarian sects." The court ruled in Dvorkin's favor and ordered Father Gleb and the other plaintiffs to pay Dvorkin 80 million rubles as restitution of legal fees. The court based its decision on testimonies of parents whose children had freely opted to convert to different religions and postings on the Internet, despite the fact that neither of these forms of evidence have legal force in Russian law, according to the Express-Chronicle newspaper.
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In 1976 he created the Christian Committee for the Defense of the Rights of Believers in the USSR. He published several hundreds of articles about the suppression of religious freedom in the Soviet Union. These documents were used by dissidents of all religious denominations. Yakunin was arrested and convicted for anti-Soviet agitation in 28 August 1980. He was kept in KGB Lefortovo prison until 1985, and then in a labor camp known as "Perm 37". Later, he was punished by involuntary settlement in Yakutia.
Gleb Yakunin was amnestied in March 1987 under Mikhail Gorbachov. He was allowed to return to Moscow and worked until 1992 again as priest. He was rehabilitated in 1991. In 1990 Yakunin was elected to the Supreme Soviet of the Russian Federation and worked as deputy chairman the Parliamentary Committee for the Freedom of Conscience. He was co-author of the law concerning "The freedom of all denominations" that was used for the opening of churches and monasteries throughout the country.
Gleb Yakunin was a member of the committee created for the investigation of the Soviet coup attempt of 1991 and chaired by Lev Ponomaryov, and thereby gained the access to secret KGB archives. In March 1992 he published materials about the cooperation the Moscow Patriarchate with the KGB. He claimed that the code names of several high-rank KGB agents in the Orthodox Church were those of Patriarch Alexius II, Mitropolitans Filaret of Kiev, Pitrim of Volokolamsk, and others. The Russian church excommunicated Yakunin in 1993, after which he joined the Ukrainian Autocephalous Orthodox Church, which regarded his excommunication as political and therefore invalid.