- Bioinformatics +1🇨🇿 NMgr. | Faculty of Science
- Computer Science with specialisation in Programming and Software Development🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Systems Programming🇨🇿 Bc. | Faculty of Mathematics and Physics
- Demography +1🇨🇿 NMgr. | Faculty of Science
- Molecular Biology and Biochemistry of Organisms🇨🇿 Bc. | Faculty of Science
- Ecological and Evolutionary Biology🇨🇿 Bc. | Faculty of Science
- Evolutionary Biology🇨🇿 NMgr. | Faculty of Science
- Teacher Education of Physical Education for Upper Secondary Schools with double curriculum study Teacher Education of Mathematics for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Physical Education and Sport
- Teacher Education of Geography for Upper Secondary Schools with double curriculum study Teacher Education of Mathematics for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- Chemistry for Teacher Education with double curriculum study Mathematics for Teacher Education🇨🇿 Bc. | Faculty of Science
- Geography for Teacher Education with double curriculum study Mathematics for Teacher Education🇨🇿 Bc. | Faculty of Science
- Physics for Teacher Education with double curriculum study Mathematics for Teacher Education🇨🇿 Bc. | Faculty of Mathematics and Physics
- Mathematics for Teacher Education with double curriculum study English Language and Literature for Teacher Education🇨🇿 Bc. | Faculty of Mathematics and Physics
- Mathematics for Teacher Education with double curriculum study Czech Language and Literature for Teacher Education🇨🇿 Bc. | Faculty of Mathematics and Physics
- Geography for Teacher Education with double curriculum study Biology for Teacher Education🇨🇿 Bc. | 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
- Applied Geobiology🇨🇿 Bc. | Faculty of Science
- Chemistry for Teacher Education with double curriculum study Biology for Teacher Education🇨🇿 Bc. | Faculty of Science