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The programme started operating in academic year 1994/95, with a different structure of subjects. Partner universities’ group was different as well in the first academic years. In 1999, University College Dublin finished its activity in the programme, and in 2000, Université des Sciences et Technologies de Lille took over its role so that the structure of partner institutions acquired today´s form. In 2002 the programme was selected by the European University Association (EUA) into the pilot project „Joint Masters in Europe“. The project was aimed at the improvement of situation in the sphere of joint academic degrees  (see also Joint European Studies Programme in the section Basic characteristics) as regards their mutual recognition in European countries, rules of awarding diplomas, etc.

By selecting EITEI in the „Joint Masters in Europe“ project, EUA appreciated its outstanding achievements in the field of multinational cooperation, the broad basis of partner universities and multidisciplinary character of studies.

By decision of the European Commission of September 2005, the M.A. in Economics of International Trade and European Integration was selected as an  ERASMUS MUNDUS master’s programme. ERASMUS MUNDUS is a programme of cooperation and mobility of students and scientific workers in the field of university studies with a view to supporting non-European students (esp. those from developing countries) during their studies in the top-quality European studies programmes. Thus, beginning in the academic year 2006/07, the participation of non-European students (see „Circle of Participants“ on this site) has increased significantly.

Since the academic year 2007/08, M.A. EITEI has been accredited as a consequential master’s programme at the Faculty of International Relations of the University of Economics, Prague (VŠE).

Since the academic year 2011/12, M.A. EGEI has been accredited as a consequential master’s programme at the Faculty of International Relations of the University of Economics, Prague (VŠE).

By decision of the European Commission of September 2012, the M.A. in Economics of Globalisation and European Integration was selected as an  ERASMUS MUNDUS master’s programme.