Abstract Cryo-electron tomography (CET) is an emerging imaging modality that is suitable for molecular and cellular structural studies. CET allows obtaining three-dimensional (3D) images of non-repetitive, that is, pleiomorphic structures, such as cells and organelles in their close-to-native state at the nanometer resolution. Here, we give an introduction to CET, ranging from the fundamentals of electron tomography and cryo preparation to state-of-the-art image processing methods used for data interpretation. We illustrate the imaging capabilities of CET by reviewing its applications ranging from reconstituted systems to intact cells. Finally, we focus on different examples where cryo-electron tomograms are correlated with different signals, such as localization of labels using light microscopy, electron-dense markers, genetic modifications, or different chemical treatments.