•Electron holographic tomography provides a unique access to 3D electric potential at the nanometer scale.•It has been successfully applied to reveal the 3D potential in nanowires and across p–n junctions in semiconductors.•The prospects of the 3D reconstruction of magnetic vector fields as well as atomic crystal potentials are discussed. The exact knowledge about intrinsic electrostatic potentials and in particular their three-dimensional distribution at the nanometer scale is a key prerequisite for understanding the solid state properties. Electron holographic tomography (EHT), the combination of off-axis holography with tomography in the transmission electron microscope, provides a unique access to this information. We review the development and application of automated EHT to reconstruct 3D potentials in nanostructures such as the mean inner potential of a material or the diffusion potential across p–n junctions in semiconductors. We also discuss future challenges of the 3D reconstruction of electric crystal potentials at atomic resolution and magnetostatic fields as well as ways to overcome present limitations of the method.