- James Franck Institute
- Janelia Farm Research Campus
- Jet Propulsion Laboratory
- Jeunes Équipes de l'Institut de Physique du Collège de France
- J. Heyrovský Institute of Physical Chemistry of the ASCR
- JIFRESSE
- Jodrell Bank Centre for Astrophysics
- Johann-Friedrich Blumenbach Institut für Zoologie und Anthropologie
- Johann Radon Institute for Computational and Applied Mathematics
- Johnson Matthey Technology Centre
- Joint Attosecond Science Laboratory
- Joint Center for Structural Genomics
- Joint Institute for Marine and Atmospheric Research
- Joint Research center
- Joseph Louis LAGRANGE
- JRC Institute for Environment and Sustainability
- Jülich Supercomputing Centre
- Julius Center for Health Sciences and Primary Care
- Juntendo University School of Medicine