- Academic Medical Center (AMC)
- Amsterdam Center for Language and Communication (ACLC)
- Center for Research in Experimental Economics and political Decision-making (CREED)
- Institute for Logic, Language and Computation (ILLC)
- Psychology Research Institute (PSYRES)
- Research Institute for Child Development and Education (CDE)
- Swammerdam Institute for Life Sciences (SILS)
Several research institutes are involved in Amsterdam Brain and Cognition (ABC)