- Headquarters
- RIKEN Next-Generation Supercomputer R&D Center
- XFEL Project Head Office
- Wako Institute
- Advanced Science Institute
- Brain Science Institute
- Nishina Center for Accelerator-Based Science
- Tsukuba Institute
- BioResource Center
- Harima Institute
- RIKEN SPring-8 Center
- Yokohama Institute
- Plant Science Center
- Center for Genomic Medicine
- Research Center for Allergy and Immunology
- Omics Science Center
- Systems and Structural Biology Center
- Bioinformatics And Systems Engineering division
- Center of Research Network for Infectious Diseases
- Kobe Institute
- Center for Developmental Biology
- Center for Molecular Imaging Science
- RIKEN Research Cluster for Innovation
- RIKEN Innovation Center
- RIKEN Program for Drug Discovery and Medical Technology Platforms
- RIKEN Biomass Engineering Program
- Computational Science Research Program
- RIKEN Advanced Institute for Computational Science
