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The Rector is the head of the University's executive body. He is nominated by the University's Academic Senate to a four-year term and appointed by the President of the Czech Republic.

The Rector appoints Deans of Faculties, Vice-Rectors for different professional fields, the Advisory Board, and Scientific Council.

The Academic Senate is elected from members of the Academic Staff and students every three years.

The Board of Directors is appointed by the Czech Republic's Ministry of Education, Youth and Sports.

Faculties are the main bodies of the University that ensure the educational, research and development activities. Authority regarding the higher educational institute is designated to the head of the institute.

The Rectorate is a complex of departments that manage the organisational, technical and financial affairs of the University.

A number of specialised centres, associations, institutions and organisations work as part of the University, and on its grounds.