- Evolutionary Biology🇨🇿 NMgr. | Faculty of Science
- Genetics, Molecular Biology and Virology with specialisation in Molecular biology and genetics of prokakaryotic and eukaryotic microorganisms🇨🇿 NMgr. | Faculty of Science
- Genetics, Molecular Biology and Virology with specialisation in Molecular biology and genetics of eukaryotes🇨🇿 NMgr. | Faculty of Science
- Zoology with specialisation in Animal Evolutionary Genetics🇨🇿 NMgr. | Faculty of Science
- Macromolecular Chemistry🇨🇿 NMgr. | Faculty of Science
- Media and Area studies🇬🇧 NMgr. | Faculty of Social Sciences
- 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 Politics and Security🇬🇧 NMgr. | Faculty of Social Sciences
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences