- BioISI | BioSystems & Integrative Sciences Institute
- CFTC | Center for Theoretical and Computational Physics
- IA | Institute of Astrophysics and Space Sciences
- IBEB | Institute of Biophysics and Biomedical Engineering
- LIP | Laboratory of Instrumentation and Experimental Particle Physics
- CENTRA - Ciências | Center for Astrophysics and Gravitation
Other Research Centres associated with the Department of Physics
- CeFEMA | Center of Physics and Engineering of Advanced Materials