- Information, media and book culture🇨🇿 NMgr. | Faculty of Arts
- History🇨🇿 Bc. | Faculty of Arts
- History – Economic and Social History🇨🇿 NMgr. | Faculty of Arts
- Bioinformatics🇨🇿 Bc. | Faculty of Science
- Evolutionary Biology🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Geochemistry🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Economic Geology🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Mineralogy and Crystallography🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Geodynamics🇨🇿 NMgr. | Faculty of Science
- Molecular Biology and Biochemistry of Organisms🇨🇿 Bc. | Faculty of Science
- Ecological and Evolutionary Biology🇨🇿 Bc. | Faculty of Science
- Parasitology and Infection Biology🇬🇧 NMgr. | Faculty of Science
- Parasitology🇨🇿 NMgr. | Faculty of Science
- Microbiology🇨🇿 NMgr. | Faculty of Science
- 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
- Master in Area Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Phonetics🇨🇿 NMgr. | Faculty of Arts
- Geology with specialisation in Paleontology🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Geology🇨🇿 NMgr. | Faculty of Science
- Computer Science with specialisation in Computer Graphics, Vision and Game Development +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Systems Programming +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- Applied Geology with specialisation in Engineering geology🇨🇿 NMgr. | Faculty of Science
- Science🇬🇧 Bc. | Faculty of Science
- Genetics, Molecular Biology and Virology with specialisation in Virology🇨🇿 NMgr. | Faculty of Science