Quantitative three-dimensional (3D) maps of large-scale structures can now be routinely obtained by the use of high- or intermediate-voltage electron tomography. The recent 3D reconstructions of the mitochondrion and the Golgi apparatus highlight both the potential and the shortcomings of this technique. New technological developments, in particular the development of automated low-dose electron tomography, are expected to facilitate the 3D visualization of large structures in the fully hydrated environment, embedded in vitreous ice.