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The University of the Aegean is spread across six scenic islands, forming a network covering all prefectures in the Aegean Archipelago, with the central administration being situated in the hills of Mytilene, the capital of Lesbos.

Though the university was only founded in 1984, its origins can be traced back to 1919, when a plan was made for the creation of a new university in Greece. The aim was to improve education opportunities outside of Athens, which was then the only educational centre in the region. It was to be called the Ionian University, but after the Greco-Turkish War of 1919 - 1922, it never opened. All those years later, the University of Aegean was created as a continuation of this initial vision.

Created with the aim of introducing new approaches to higher education through interdisciplinary subject areas to fit the needs of the contemporary world, many of the courses cover new scientific domains, with names such as Communication Systems, Cultural Informatics, Education Design, and Mediterranean Studies. Postgraduate programmes, aimed at an international level, fall under such subject areas as European Integration, Biodiversity, and Environmental Policy and Management.
While most courses are taught in Greek, there are some bilingual MSc programmes, and personal support may be offered in languages such as English, French, German, or Turkish. Since 2004 the School of Social Sciences has hosted Modern Greek language classes throughout the academic year.

As an active member of the European Universities Association, a founding partner of the Cremo network, a member of the EMUNI Senate, a collaborator in many academic and research networks, and participant in more than 210 bilateral and LLP Erasmus academic agreements, the university has strived to create a strong international academic and research profile.