One of the very first criminal proceedings initiated under the section of crimes against humanity by the Estonian Internal Security Service in January 1995 was the investigation of the March deportation. On 25-29 March 1949 more than 20 000 people were deported from Estonia to Siberia in the course of the joint operation "Priboi" ("Breaker") organised by the USSR Ministry of State Security (MGB) and the Ministry of Internal Affairs (MVD).
In the investigation of the March deportation the first judicial decision was reached on 22 January 1999 when the Lääne County Court convicted a former operational commissioner of the Lääne County Department of the Estonian SSR MGB Johannes Klaassepp (1921-2010) of the deportation of 23 persons and attempted deportation of 9 persons from Läänemaa in 1949, sentencing him to 8 years suspended imprisonment with a probation period of 2 years. The Tallinn Circuit Court partially satisfied the appeal submitted by J. Klaassepp, finding evidence for the deportation of 15 persons and attempted deportation of 2 persons, but the judgement remained unaltered.
By the decision of the Pärnu County Court of 10 March 1999 a former Pärnu County operational commissioner of the ESSR MGB Vassili Beskov (1918) was convicted of the deportation of 7 families (21 persons) and attempted deportation of 2 families and he was sentenced to 2 years suspended imprisonment with a probation period of 3 years.
On 30 July 1999 the Pärnu County Court convicted a former Pärnu County operational commissioner of the ESSR MGB Mihhail Neverovski (1920-2000) of identifying 75 families or 278 persons who were then deported. According to the court decision M. Neverovski participated personally in the deportation of 8 persons and in the attempted deportation of 2 persons and he was sentenced to 4 years imprisonment. On 1 November 1999 the Tallinn Circuit Court replaced his actual imprisonment by 4 years suspended imprisonment with a probation period of 3 years.
On 17 March 1999 the Järve County Court proved a former operational commissioner of the Järva County Department of the ESSR MGB Vladimir Loginov (1924-2001) guilty of crimes against humanity (deportation of 16 persons) and terminated the criminal proceeding. Based on the court decision V. Loginov was placed in inpatient psychiatric hospital for coercive treatment until recovery.
By the judgement of the Tallinn City Court a former senior operational commissioner of the Harju County of the ESSR MGB Juri Karpov (1921-2012) was convicted of the deportation of 40 persons and attempted deportation of 20 persons. The Tallinn City Court did not satisfy the appeal of J. Karpov on 19 December 2002 and the judgement of the Tallinn City Court remained in force. The Supreme Court did not grant the appeal in cassation submitted by J. Karpov the leave to appeal, thus the judgment by the Tallinn City Court to sentence J. Karpov to 8 years suspended imprisonment with a probation period of 3 years took effect.
On 10 October 2003 the Saare County Court convicted operational commissioner of the central headquarters of the ESSR MGB August Kolk (1924) and militiamen of the Saare County Department of the ESSR MVD Pjotr Kislõi(1921) of the deportation carried out on the island of Saaremaa in 1949 and sentenced them to 8 years suspended imprisonment with a probation period of 3 years for the commission of crimes against humanity. Both the Tallinn Circuit Court on 27 January 2004 and the Supreme Court on 21 April 2004 rejected the appeal submitted by A. Kolk and P. Kislõi and the court judgement remained in force. On 17 January 2006 the European Court of Human Rights did not grant the appeal submitted by A. Kolk and P. Kislõi against the Republic of Estonia the leave to appeal.
On 7 November 2006 the Saare County Court convicted militiamen of the Saare County Department of the ESSR MVD Vladimir Kask (1926) of crimes against humanity and sentenced him to 8 years suspended imprisonment with a probation period of 3 years.
At the end of 1998 the Internal Security Service initiated criminal proceedings to investigate the activities of a former assassin agent of the ESSR MGB Karl-Leonhard Paulov (1924-2002). The pre-trial investigation ascertained that as an agent of the MGB K.-L. Paulov killed the civilian Aleksander Sibul in Võru County, rural municipality of Veriora, on 18 October 1945 and the civilians Alfred Pärl and Aksel Pärl on 27 October 1946. During the trial the Põlva County Court re-qualified the act committed by K.-L. Paulov as murder for the purpose of personal gain. The Tartu Circuit Court did not alter the court judgement but the Supreme Court annulled the judgements made by the Põlva County Court and the Tartu Circuit Court and remitted the case to the Põlva County Court with a different panel composition for a second hearing. On 29 July 2000 the Põlva County Court convicted K.-L. Paulov of crimes against humanity and sentenced him to 8 years imprisonment in maximum-security prison. The Tartu Circuit Court did not alter the judgement of the Põlva County Court on 5 October 2000 and the Appeals Selection Committee of the Supreme Court did not grant the appeal in cassation the leave to appeal. Thus, the penalty of 8 years imprisonment imposed upon K.-L. Paulov entered into force. It is also the only occasion when Estonian courts have sentenced a person who has committed a crime against humanity to actual imprisonment. K.-L. Paulov died of old age on 6 February 2002 while serving his sentence in Murru prison.
As for the other criminal cases related to the murder of forest brothers, on 2 September 2003 the Tartu Circuit Court convicted the former Head of the Elva District Department of the ESSR Ministry of Internal Affairs Vladimir Penart(1925) and his assassin agent Rudolf Tuvi (1925-2008) of murdering the civilians Oskar Rumm, Vendo Saks and Paul Miks in Elva in 1953-1954. On 18 December 2003 the Supreme Court did not grant the appeal in cassation submitted by V. Penart the leave to appeal. On 29 March 2004 V. Penart lodged an appeal with the European Court of Human Rights against the Republic of Estonia but the Court refused the appellant's demand to appeal, providing a well-reasoned decision for it.
In the summer of the same year also August Kolk and Pjotr Kislõi convicted of the Saaremaa deportation of 1949 lodged an appeal with the European Court of Human Rights against the Republic of Estonia. The content of the appeals and the legal reasons provided by the Court were identical in both cases.
The appellants emphasized that pursuant to the principles of criminal law a person is not punishable for an act that was not a crime pursuant to the law in force at the time of its commission. The European Court of Human Rights, on the contrary, confirmed in its decisions of 17 January 2006 and 24 January 2006 that murdering and deporting of civilians was recognised as a crime against humanity already under Article 6c of the Charter of the Nürnberg Tribunal of 1945. In its decision the European Court of Human Rights equalized in essence the crimes of Communism and Nazism, corroborating that the same international principles and legal sources apply for both. The court came to the conclusion that even if the acts committed by V. Penart, A. Kolk and P. Kislõi were regarded as "lawful" pursuant to the Soviet law, they were however crimes against humanity pursuant to the international law. Additionally, the court noted that Estonia was occupied by the Soviet Union in 1940-1941 and 1944-1991 and in these periods the totalitarian occupation regime conducted large-scale and systematic repressions against the Estonian population.