Since the early beginning of the integrated circuits, electromigration is a reliability issue of first interest. In 3-dimensional structures, electromigration is responsible for the formation of voids in lines connected to the Through Silicon Via (TSV). To our knowledge, this paper presents the first in operando electromigration experiment in a Scanning Electron Microscope (SEM) performed for 3D integration. The experimental protocol, including sample preparation and temperature regulation, is detailed. A current of 25 mA is injected in a structure heated at 350 °C for about 900 h. The evolution of voids is monitored and explained. Void growth occurs step by step, so that the microstructure may be assumed to play a major role in the depletion mechanism. The behavior of the electrical resistance is analyzed using the SEM micrographs.