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AAPA was founded in 1912 at a New York City conference of public port officials from 11 U.S. ports. The meeting was called to exchange ideas relative to port organization, to promote the exchange of information and the development of uniform methods of administration and possibly to provide for some permanent organization between the principal port authorities.

Within three years, members of the National Association of Port Authorities voted to extend membership eligibility to ports throughout the Western Hemisphere and accordingly renamed it the American Association of Port Authorities. By 1914, AAPA welcomed its first Canadian member; in 1921 the first Latin American port member joined and in 1949 the first Caribbean port member joined the Association.

The Association was incorporated on March 24, 1930. In 1947 AAPA established permanent offices in Washington, D.C. and in 1949 the Association hired its first full-time executive director.

AAPA remained headquartered in Washington, D.C. until 1984 when it relocated to Alexandria, Virginia. In 2021, AAPA moved to office space in Washington, D.C., strategically located between Washington Reagan National Airport and Capitol Hill.