The Netherlands Institute for Neuroscience has seventeen research groups. They are part of the NIN community and join (group)meetings, seminars and social events. All seventeen groups are housed in the NIN buildings and use the (lab)facilities and other services provided by the NIN. The employees of fourteen groups are employed at the NIN and led by the NIN director. The employees of three groups are employed at the AMC and (formally) led by AMC management. Current director of the NIN is Pieter Roelfsema. Vice-director is Chris de Zeeuw.

The NIN aims to establish a flat management culture, in which all PIs, young talents and support staff feel free to communicate at all levels of the organization and in which all can develop their academic and technical skills and prosper.

A organization chart of the research groups at the NIN