- Centre for Ibero-American Studies
- Czech Institute of Egyptology
- Department of Adult Education and Personnel Management
- Department of Aestetics
- Department of Anglophone Literatures and Cultures
- Department of Archaeology
- Department of Auxiliary Historical Sciences and Archive Studies
- Department of Central European Studies
- Department of Culturology
- Department of Education
- Department of Linguistics
- Department of Logic
- Department of Physical Education
- Department of Psychology
- Department of Social Work
- Department of Sociology
- Department of South Slavonic and Balkan Studies
- Department of the English Language and ELT Methodology
- Department of Theatre Studies
- Film Studies Department
- Institute for Classical Archeology
- Institute for Greek and Latin Studies
- Institute of Art History
- Institute of Comparative Linguistics
- Institute of Czech and Comparative Literature and Literary Theory
- Institute of Czech History
- Institute of Czech Language and Theory of Communication
- Institute of Czech Studies
- Institute of East Asian Studies
- Institute of East-European Studies
- Institute of Economic and Social History
- Institute of Ethnology
- Institute of General History
- Institute of Germanic Studies
- Institute of Information Studies and Librarianship
- Institute of Musicology
- Institute of Near Eastern and African Studies
- Institute of Philosophy and Religious Studies
- Institute of Phonetics
- Institute of Political Science
- Institute of Romance Studies
- Institute of South and Central Asia
- Institute of the Czech National Corpus
- Institute of Theoretical and Computational Linguistics
- Institute of Translation Studies
- Language Centre
Centres and Specialized Departments
Gallery of Ancient Art in Hostinné
Gallery of Ancient Art and Architecture in Litomyšl