- Law and Jurisprudence🇨🇿 Mgr. | Faculty of Law
- Child and Adult Nutrition🇨🇿 NMgr. | First Faculty of Medicine
- 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
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences
- Geology with specialisation in Economic Geology🇨🇿 NMgr. | Faculty of Science
- Geology with specialisation in Mineralogy and Crystallography🇨🇿 NMgr. | Faculty of Science
- Mathematical Modelling in Physics and Technology🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Physics🇨🇿 Bc. | Faculty of Mathematics and Physics
- Area Studies with specialisation in Area Studies +1🇨🇿 Bc. | Faculty of Social Sciences
- Czech-German Studies🇨🇿 Bc. | Faculty of Social Sciences
- Teacher Education of Geography for Upper Secondary Schools with double curriculum study Teacher Education of Biology for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- Molecular Biology and Biochemistry of Organisms🇨🇿 Bc. | Faculty of Science
- Applied Geobiology🇨🇿 Bc. | Faculty of Science
- Ecological and Evolutionary Biology🇨🇿 Bc. | Faculty of Science
- Teacher Education of Biology for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- Teacher Education of Chemistry for Upper Secondary Schools with double curriculum study Teacher Education of Biology for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- Earth Sciences🇨🇿 Bc. | Faculty of Science
- Geology with specialisation in Geoarchaeology🇨🇿 Bc. | Faculty of Science
- Teacher Education of Chemistry for Upper Secondary Schools with double curriculum study Teacher Education of Geology for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- Mathematics for Teacher Education with double curriculum study Physical Education for Teacher Education🇨🇿 Bc. | Faculty of Education
- Biologie, geologie a environmentalistika se zaměřením na vzdělávání with double curriculum study Physical Education for Teacher Education🇨🇿 Bc. | Faculty of Education
- Information and Communication Technology for Teacher Education with double curriculum study Physical Education for Teacher Education🇨🇿 Bc. | Faculty of Education
- Social Sciences for Teacher Education with double curriculum study Physical Education for Teacher Education🇨🇿 Bc. | Faculty of Education
- Education towards Health for Teacher Education with double curriculum study Physical Education for Teacher Education🇨🇿 Bc. | Faculty of Education
- International Master in Security, Intelligence and Strategic Studies (IMSISS)🇬🇧 NMgr. | Faculty of Social Sciences