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The discussion on the establishment of a judicial cooperation unit was first introduced at a European Council Meeting in Tampere, Finland, on 15 and 16 October 1999, attended by heads of state and government. This meeting was dedicated to the creation of an area of freedom, security and justice in the European Union, based on solidarity and on the reinforcement of the fight against trans-border crime by consolidating cooperation among authorities.

To reinforce the fight against serious organised crime, the European Council, in its Conclusion 46, agreed that a unit (Eurojust) should be set up, composed of national prosecutors, magistrates, or police officers of equivalent competence, detached from each Member State according to its own legal system.

On 14 December 2000, on the initiative of Portugal, France, Sweden and Belgium, a provisional judicial cooperation unit was formed under the name Pro-Eurojust, operating from the Council building in Brussels. National Members were then called National Correspondents. This unit was the forerunner of Eurojust, the purpose of which was to be a sounding board of prosecutors from all Member States, and where Eurojust’s principles would be tried and tested.

Pro-Eurojust formally commenced operations on 1 March 2001 under the Swedish Presidency of the European Union.

With the attacks of 9/11 in the USA, the focus on the fight against terrorism moved from the regional/national sphere to its widest international context and served as a catalyst for the formalisation, by Council Decision 2002/187/JHA, of the establishment of Eurojust as a judicial coordination unit. In the first half of 2002, during the Spanish Presidency of the EU, important milestones were reached: the Eurojust Decision was published on 28 February, the budget was released in May, and the Rules of Procedure were agreed upon in June.

Since 2002, Eurojust has grown tremendously and so have its operational tasks and involvement in European judicial cooperation. More powers and a revised set of rules became necessary.

On 29 April 2003, Eurojust moved to its seat in The Hague. Shortly after its establishment, Eurojust faced the challenge of EU enlargement: in May 2004, ten new National Members joined the College, two more joined in January 2007, and the last joined in July 2013, bringing the total number of National Members to 28. Eurojust has also been active in negotiating cooperation agreements with third States and other EU agencies, which allowed the exchange of judicial information and personal data. Agreements were concluded with, among others, Europol, Norway, Iceland, the USA, OLAF, Switzerland, North Macedonia (formerly fYROM), Moldova, Montenegro and Ukraine. Liaison prosecutors were appointed for Norway, the USA, Switzerland, Montenegro, Ukraine and North Macedonia. In addition to cooperation agreements, Eurojust also maintains a network of contact points worldwide.

In July 2008, under the French Presidency, the European Council approved the new Council Decision on the Strengthening of Eurojust, which was ratified in December 2008 and published on 4 June 2009. The new Decision’s purpose was to enhance the operational capabilities of Eurojust, increase the exchange of information between the interested parties, facilitate and strengthen cooperation between national authorities and Eurojust, and strengthen and establish relationships with partners and third States.

The Lisbon Treaty contained an important chapter in the development of Eurojust in its Article 85, which mentions Eurojust and defines its mission, ‘to support and strengthen coordination and cooperation between national investigating and prosecuting authorities in relation to serious crime affecting two or more Member States […]’.

In July 2013, the European Commission submitted a proposal to the European Parliament and the Council for a new regulation on Eurojust to provide a ‘single and renovated legal framework for a new Agency for Criminal Justice Cooperation (Eurojust)’, the legal successor of Eurojust as established in 2002.

After extensive negotiations, the European Parliament and the Council adopted the Regulation on the European Union Agency for Criminal Justice Cooperation in November 2018. The Regulation established a new governance system, clarified the relationship between Eurojust and the European Public Prosecutor’s Office, prescribed a new data protection regime, adopted new rules for Eurojust’s external relations and strengthened the role of the European and national Parliaments in the democratic oversight of Eurojust’s activities. The application of the Regulation started on 12 December 2019.

As Denmark does not participate in the Eurojust Regulation, the number of National Desks decreased in December 2019 to 27, with Denmark delegating a Representative to Eurojust.
After the withdrawal of the United Kingdom from the European Union on 31 January 2020, the number of National Desks is 26.