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The Centre for Applied Ethics has its origin in the "Aula de Ética Social" that began at the University of Deusto at the beginning of the 1993/94 academic year. The aim of the Aula was to develop the UD’s University Project regarding the promotion of the values underpinning human dignity. In the 1996/97 academic year, Xabier Etxeberría was appointed director and held this position until late 2010, when José María Guibert took over until 2013.

In its first stage, the Aula de Ética focused on promoting a compulsory subject on professional ethics in all the University's degree programmes, as well as on training lecturers to ensure that this subject was adequately taught.

Since its inception, the Aula de Ética has encouraged the University’s public presence in social issues and problems with an ethical background. Along these lines, the Centre for Applied Ethics has addressed issues such as terrorist violence and its victims, ethical banking, social responsibility, or the rights of people with disabilities.

With a view to disseminating and giving outreach to research findings, in the 1995-96 academic year the Aula de Ética launched a collection of "Cuadernos de Ética" published by the University's own publishing house.

From the beginning, the Aula was integrated into national and international networks such as UNIJES, AUSJAL, Metanexus, EBEN, FUCE and, through the latter, into the European Ethics Network. Partnerships and joint initiatives have been particularly intense with Latin American universities, and bilateral collaboration agreements were signed with the Instituto Tecnológico y de Estudios Superiores de Monterrey (ITESM - Mexico), the Universidad Católica de Temuco, and the Universidad Católica de Valparaíso.

In 2008, the University acknowledged the research effort made by the Aula de Ética by officially recognising the "Ethics applied to social reality" team, with three research areas: social and political ethics, organisational ethics, cooperativism, and social and solidarity economy. By taking this step, the University recognised the quality of the team's research. In 2010, the team was recognised by the Basque Government.

The Centre for Applied Ethics was created in December 2009, which opened up the possibility of designing and developing postgraduate programmes, and enhanced research and knowledge transfer.