Silicon nanoclusters (Si-nc) embedded in SiO2 matrix have recently attracted much interest as potential candidate for many applications compatible with CMOS processing: photovoltaic cells, memory devices, waveguide amplifiers... Light emission and carrier storage properties exhibited by Si-nc are directly linked to the clusters characteristics (size, distribution, composition, interface nature with surrounding matrix...). Therefore, an accurate control of these parameters is essential in order to improve these systems. Conventional spectroscopy and microscopy techniques often encounter some limits to give quantitative information about Si-nc, especially when clusters are not crystalline. Atom probe tomography (APT) provides a 3D chemical mapping of the analyzed material at atomic scale (crystalline or not). Since the implementation of laser to APT, it becomes possible to analyze semi-conductors and oxides. In the case of Si-nc embedded in silica, APT is able to provide an accurate measurement of precipitate diameter, distribution and interface composition. Accessing this level of accuracy will help to understand and control the Si-nc characteristics which govern the properties of these new materials. The principle of the Atom probe Tomography technique will also be presented as well as its contribution in this field.