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The Estonian Air Line Pilots Association  (Estonian APLA) was founded on the 15th of March 1990 based on the charter adopted in the foundation meeting. The charter was amended on the 13th of September that same year and Estonian APLA was registered by a resolution of the Supreme Council of the Republic of Estonia on the 16th of October 1990.
Until 1995 Estonian APLA’s membership consisted of air line pilots working in the Government of Estonian Civil Aviation.  In 1996 stewardesses/stewards joined the organization and in 2001 stewardesses/stewards founded Estonian Stewardesses and Stewards Trade Union (ESSTU).
 The size of the membership upon founding was 193 pilots (180 in Tallinn and 13 in Tartu).  Between 1993-1996 there were multiple changes in aviation resulting in a membership decrease to 120 members.
After the founding of ESSTU in 2001, Estonian APLA had 34 pilots. Further development had increased the membership to 52 members by the year 2005.
During the entire functioning of Estonian APLA, management has considered it important to co-operate with other trade unions both in Estonia and abroad. Since the foundation, Estonian APLA has been a member of the Confederation of Estonian Trade Unions (CETU). Starting from 6th of April 1992, Estonian APLA has been a member of International Federation of AirLine Pilots’ Associations (IFALPA).  
Due to the close co-operation with trade unions of transportation sector, Estonian APLA became a member of the Federation of Transport Workers’ Trade Unions (FTWTU).
Since 2003 co-operation has been tightened with European Cockpit Association (ECA).  Starting from 2004, EAPTU has been taking part in the work of SAS Group Pilots Association (SAGPA) as an observer member.
Together with a need to develop the co-operation among trade unions of aviation sector, members of Estonian APLA and ESSTU founded Estonian Airline Aviation Trade Union (EAATU) which represents EAPTU in CETU and FTWTU since spring 2005.
On October 6 2005 Estonian APLA became a member of the Strike Treaty.