- ATOMIN – Atomic Scale Science for Innovative Economy
- BeMoT – Direct monitoring of strain for protection of historic textiles and paintings on canvas
- NANOSAM – Centre for Nanometer-scale Science and Advanced Materials
- National Synchrotron Radiation Centre SOLARIS
- EGA – European Games Academy
- Ordered programmes of study
- NLTK – National Laboratory of Quantum Technologies
- TEAM Programme – Coherently prepared media – novel properties and applications
- TEAM - Correlations and coherence in quantum materials and structures (CCQM) - unique properties on macro and nano scales
- WIKING – Knowledge and competence in physics, chemistry and computer science for economy
- Fibonacci – Designing, implementing and formalizing the process of dissemination of inquiry-based teaching and learning methods in science and mathematics in primary and secondary schools in Europe
- MRPO - Modernization of teaching infrastructure for the first-cycle programmes in exact and natural sciences at the JU