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To fabricate and qualify nanodevices, characterization tools must be developed to provide a large panel of information over spatial scales spanning from the millimeter down to the nanometer. Synchrotron x-ray-based tomography techniques are getting increasing interest since they can provide fully three-dimensional (3D) images of morphology, elemental distribution, and crystallinity of a sample. Here we show that by combining suitable scanning schemes together with high brilliance x-ray nanobeams, such multispectral 3D volumes can be obtained during a single analysis in a very efficient and nondestructive way. We also show that, unlike other techniques, hard x-ray nanotomography allows reconstructing the elemental distribution over a wide range of atomic number and offers truly depth resolution capabilities. The sensitivity, 3D resolution, and complementarity of our approach make hard x-ray nanotomography an essential characterization tool for a large panel of scientific domains.