- Scandinavian Studies🇨🇿 NMgr. | Faculty of Arts
- General Linguistics — Scandinavian Studies🇨🇿 NMgr. | Faculty of Arts
- Geology with specialisation in Geochemistry🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Geoarchaeology🇨🇿 NMgr. | Faculty of Science
- Particle and Nuclear Physics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Genetics, Molecular Biology and Virology with specialisation in Virology🇨🇿 NMgr. | Faculty of Science
- Sociology with specialisation in Sociology🇨🇿 Bc. | Faculty of Arts
- Sociology with specialisation in Sociology with Economics🇨🇿 Bc. | Faculty of Arts
- Sociology🇨🇿 NMgr. | Faculty of Arts
- Area Studies with specialisation in Balkan, Eurasian and Central European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in German and Austrian Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in North American Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in West European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Balkan, Eurasian and Central European Studies with specialisation in Russian and Eurasian Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Balkan, Eurasian and Central European Studies with specialisation in Balkan and Central European Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Master in Area Studies🇬🇧 NMgr. | Faculty of Social Sciences
- International Masters in Economy, State and Society with specialisation in History and Society🇬🇧 NMgr. | Faculty of Social Sciences
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences