In combination with nuclear microprobes, STIM and PIXE tomography offer non-destructive quantitative three-dimensional characterization of microscopic samples. STIM tomography provides 3D density maps of the analyzed sample with sub-micrometer resolution and PIXE tomography is one of the only methods allowing a quantification of trace elements in three dimensions. These tomography techniques have been developed in several microbeam laboratories around the world since the 80’s. Nevertheless, despite a huge interest in mapping the inner content of a sample without destroying it, the use of ion beam tomography has been limited to a few studies up to now. This comes from the specific requirements of this kind of experiments, i.e. specific experimental set-up (rotation of the sample during analysis) and reconstruction software, making this type of experiments difficult to handle and relatively long. For a few years, efforts have been made to facilitate the implementation of these techniques and reduce the duration of data acquisition: new detectors and new algorithms were proposed. After an introduction to ion beam tomography techniques and to the first developments made in that field, the experimental and data processing specificities of this 3D imaging approach will be discussed. Finally, examples of recent applications to biology and material science are presented, as well as related techniques developed in the field of microbeam 3D imaging.Read less <