- 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" (website in Polish)
- Nature Education Centre
- Jagiellonian University Press
- Centre for Digital Medicine and Robotics
- Jagiellonian Centre for Digital Humanities
- Centre for Brain Research
- Biobank of the Jagiellonian University - Medical College
- Centre for Innovative Medical Education (website in Polish)