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Division of Elementary Particle Physics
- Department of Astroparticle Physics (16)
- Department of Experimental Particle Physics (22)
- Department of Particle Theory and Cosmology (29)
- Department of Detector Development and Data Processing (33)
- Department of Cosmology and gravitational physics (39)
Division of Condensed Matter Physics
- Department of Magnetic Measurements and Materials (11)
- Department of Dielectrics (12)
- Department of Material Analysis (17)
- Department of Functional Materials (18)
- Department of Condensed Matter Theory (23)
- Department of Chemistry (32)
Division of Solid State Physics
- Department of surfaces and molecular structures (13)
- Department of Semiconductors (14)
- Department of Spintronics and Nanoelectronics (15)
- Department of Structure Analysis (19)
- Department of Magnetics and Superconductors (24)
- Department of Thin Films and Nanostructures (26)
- Department of Optical Materials (27)
Division of Optics
- Department of optical and biophysical systems (21)
- Department of Low-Temperature Plasma (25)
- Department of Analysis of Functional Materials (28)
- Optical and Mechanical Workshops Na Slovance (31)
- Joint Laboratory of Optics (38)
Division of High Power Systems
- Department of Radiation and Chemical Physics (52)
- Department of Technical Support (55)
- Department of Engineering and Technical Support (57)
- Department of Projects Management (58)
- Department of Advanced Laser Development (61)
- Department of Industrial Laser Applications (62)
- Department of Scientific Laser Applications (63)
Central Unit
- Secretariate of the Director (10)
- Computing and Networking Department (20)
- Scientific Library Na Slovance (71)
Administration Unit (AU)
- Technical Department (34)
- Finance Department (40)
- Cost Accounting Department (41)
- Personnel and Payroll Department (42)
- Supply and Transport Department (43)
- Department of Support of AU (49)
Administrative Unit Cukrovarnická
- Mechanical Workshop Cukrovarnická (30)
- Administrative Department Cukrovarnická (44)
- Scientific Library Cukrovarnická (72)
ELI Beamlines Project Division
- Department of Radiation Physics and Electron Acceleration (86)
- Department of Ion Acceleration and Applications of High Energy Particles (87)
- Department of Structural Dynamics (88)
- Department of Plasma Physics and Ultra-high Intensity Interactions (89)
- Department of Laser Systems (91)
- Department of Construction and Design Support (93)
- Department of Administration (94)
- Department of the ELI Beamlines Facility Director’s Office (96)
- Department of Technical Infrastructure and Instrumentation Services (97)
- Department of Technology Transfer – CITT (98)
- Department of Building Infrastructure and IT (99)