Nencki Institute includes 31 research and 10 core-facility laboratories. Research laboratories of the Institute operate within two scientific centres: Center for Basic and Translational Research in Biology and Biomedical Sciences, and Center for Neural Plasticity and Brain Disorders BRAINCITY. Core-facility environmental laboratories are grouped within Neurobiology Center. Moreover, Institute owns a field Research Station in Mikolajki which provides an infrastructure for field and behavioural research.

The scientific activity of the Nencki Institute scientists is supported by qualified and devoted employees of Administration and Supporting Units.