Henning Stahlberg studied physics at the Technische Universität Berlin and graduated with a doctorate from the Swiss Federal Institute of Technology in Lausanne (EPFL) in 1997.

From 2009 to 2020, Stahlberg was a Full Professor for Structural Biology at the Biozentrum of the University of Basel, where he headed the Center for Cellular Imaging and NanoAnalytics (C-CINA).

He heads the Laboratory of Biological Microscopy at the EPFL and is establishing the Dubochet Center for Imaging in Lausanne.

Employing cryo-electron microscopy, electron tomography, and correlative light and electron microscopy CLEM, he investigates the structure of ion channels[3] and membrane transporters,[4] and studies the molecular and cellular events in Parkinson's disease.

Using these methods, Stahlberg successfully elucidated among other things the 3D structure of the Type III Secretion System (T3SS) in intact bacteria.