This contribution deals with the morphological and elemental characterisation with high-energy (MeV) focused ion beams (in particular protons) with special emphasis on high spatial resolution in the sub-micrometer regime and very low minimum detection limits (sub-ppm) in trace element analysis. The. most important methods like particle induced X-ray emission (PIXE), Rutherford backscattering spectrometry. (RBS), as well as scanning transmission ion microscopy (STIM) and STIM-tomography will be illustrated by examples from material and life sciences. (c) 2005 Elsevier B.V. All rights reserved.