- JU Archives (website in Polish)
- Jagiellonian Library
- MC Medical Library
- Jagiellonian Centre for Experimental Therapeutics
- Małopolska Centre of Biotechnology
- JU Museum
- Teacher Training Centre (website in Polish)
- Jagiellonian University of the Third Age (website in Polish)
- Jagiellonian Language Centre
- JU MC Postdiploma Medical Training Centre (website in Polish)
- JU Sports Centre (website in Polish)
- MC Sports Centre (website in Polish)
- Synchrotron Radiation Centre "Solaris"
- Center for Quantitative Research in Political Science
- Jagiellonian Centre for Migration Studies
- JU Medical College Language Centre (website in Polish)
- Natural Science Library (website in Polish)
- The Jagiellonian University Polish Research Centre in London (website in Polish)
- Jagiellonian Centre for African Studies
- Centre for Integrated Systems Development (website in Polish)
- The Jagiellonian Centre for Interdisciplinary Studies on Culture
- Centre for Technology Transfer CITTRU
- Copernicus Center for Interdisciplinary Studies
- Jagiellonian Center for Law, Language and Philosophy
- Experimental Farming Centre "Łazy"
- Nature Education Centre
- Jagiellonian University Press
- Centre for Digital Medicine and Robotics
- Jagiellonian Centre for Digital Humanities
- Centre for Brain Research
- Centre for Innovative Medical Education (website in Polish)
- Ars Docendi Centre for Educational Excellence (website in Polish)
- Centre for the Development of Treatments for Diseases of Affluence and Age-Related Diseases (website in Polish)
- Centre for Research on Higher Education (website in Polish)
- Jagiellonian Center for Artificial Intelligence
- Interdisciplinary Health Data Center
- Center for the Humanitarian Medicine
- Jagiellonian Centre for Clinical Research
- Campus Living Lab Useful Research Hub
- Jagiellonian Centre for Research on the Berlin Collections
- Jagiellonian Center for Diplomacy