After 1989 most of separate faculties in regional cities became standalone universities. They usually bear name of the region. Technology universities in Ostrava, Pilsen and Liberec opened more faculties and branches of study, including humanities, and changed their names.
- University of Pardubice – founded in 1950 as the Chemistry College later for 40 years known as the Institute of Chemical Technology.
- University of West Bohemia – founded in 1990 (continuation of University of Mechanical and Electrotechnical Engineering, est. 1949 under ČVUT, independent 1953).
- University of South Bohemia in České Budějovice – founded in 1991.
- University of Ostrava – founded in 1991 (continuation of Higher School of Education, est. 1953).
- Jan Evangelista Purkyně University in Ústí nad Labem – founded in 1991. Purkyně was a biologist, one of the best Bohemian scholars of 19th century.
- University of Silesia, Opava – founded in 1991.
- Technical University of Liberec – founded 1994 (continuation of University of Mechanical and Textile Engineering, est. 1953).
- University of Hradec Králové – founded in 2000 (renamed in 2000, continuation of independent Faculty of Education, est. 1964).
- Tomas Bata University in Zlín – founded in 2001.
(Universities that no longer exist)
- Law University in Prague: established by separation of Law faculty of Prague University during the 1360s. In long-lasting religious wars in Bohemia (Hussite Wars, after 1420) Law University ended its being.
- Prague German University: because of both-sided language chauvinism between Prague Bohemians and Germans, the old Prague University was divided into two Universities of two languages in 1882. Important scholars have taught there, e.g. Albert Einstein, Christian von Ehrenfels or Hans Kelsen. In the 1930s University got slowly under Nazi influence (rector San Niccolo). In 1945, University was closed by government.
- Russian Free University in Prague: this University was established in the 1920s and financed by Government of Czechoslovakia to help Russian emigrants who fled before Bolsheviks from their home country. University was closed by German Occupants in 1939 and by second time in 1945 by new leftist government. Many Russian professors and other Russian emigrees, citizens of Czechoslovakia, were kidnapped to Soviet Russia by NKVD in 1945.
- Ukrainian Free School in Prague: this university school was established in the 1920s for Ukrainians who fled before Bolsheviks. School followed the end of Russian Free University, many Ukrainian emigres were also kidnapped by NKVD.
This is a list of all universities in the Czech Republic as of April 2005. It also includes small ones.
- Academy of Performing Arts in Prague (Akademie múzických umění v Praze, AMU)
- Academy of Fine Arts, Prague (Akademie výtvarných umění v Praze, AVU)
- Czech Technical University in Prague (České vysoké učení technické v Praze, ČVUT)
- Czech University of Life Sciences Prague (Česká zemědělská univerzita v Praze, ČZU)
- Janáček Academy of Music and Performing Arts (Janáčkova akademie múzických umění, JAMU)
- University of South Bohemia in České Budějovice (Jihočeská univerzita v Českých Budějovicích, JČU)
- Masaryk University (Masarykova univerzita v Brně, MU)
- Mendel University Brno (Mendelova univerzita v Brně, MENDELU)
- University of Ostrava (Ostravská univerzita v Ostravě, OU)
- Silesian University (Opava) (Slezská univerzita v Opavě, SU)
- Technical University of Liberec (Technická univerzita v Liberci, TUL)
- University of Hradec Králové (Univerzita Hradec Králové, UHK)
- Jan Evangelista Purkyně University in Ústí nad Labem (Univerzita Jana Evangelisty Purkyně v Ústí nad Labem, UJEP)
- Charles University in Prague (Univerzita Karlova v Praze, UK)
- Palacký University of Olomouc (Univerzita Palackého v Olomouci, UP)
- University of Pardubice (Univerzita Pardubice, UPA)
- Tomas Bata University in Zlín (Univerzita Tomáše Bati ve Zlíně, UTB)
- University of Veterinary and Pharmaceutical Sciences, Brno (Veterinární a farmaceutická univerzita v Brně, VFU)
- Technical University of Ostrava (Vysoká škola báňská – Technická univerzita Ostrava, VŠB – TUO)
- University of Economics, Prague (Vysoká škola ekonomická v Praze, VŠE)
- Institute of Chemical Technology in Prague (Vysoká škola chemicko-technologická v Praze, VŠCHT)
- College of Polytechnics Jihlava (Vysoká škola polytechnická Jihlava, VŠPJ)
- Institute of Technology and Business (Vysoká škola technická a ekonomická v Českých Budějovicích, VŠTE)
- Academy of Arts, Architecture and Design in Prague (Vysoká škola uměleckoprůmyslová v Praze, VŠUP)
- Brno University of Technology (Vysoké učení technické v Brně, VUT)
- University of West Bohemia (Západočeská univerzita v Plzni, ZČU)
- Police Academy (Policejní akademie České Republiky)
- University of Defence (Univerzita obrany) in Brno, Vyškov and Hradec Králové.
- Jan Amos Komensky University
- University of New York in Prague, s.r.o.
- New York University – NYU Prague
- Škoda Auto University