Depth profiles of Si nanocrystals formed in sapphire by ion implantation and the effect of charging during X-ray Photoelectron Spectroscopy (XPS) and Secondary Ion Mass Spectrometry (SIMS) measurements have been studied. Atomic concentration and the chemical environment of Si, Al, and O have been measured as a function of depth from the sample surface by SIMS and XPS. Both as-implanted and annealed samples have been analyzed to understand the effect of nanocrystal formation on the depth distribution, chemical structure, and the charging effect before and after the formation process. SIMS measurements have revealed that the peak position of the Si concentration shifts to deeper values with implantation dose. This is explained by the fact that the structure of the matrix undergoes a phase transformation from pure sapphire to a Si rich amorphous Al2O3 with heavy dose implantation. Formation of Si nanocrystals has been observed by XPS by an increase in the Si-Si signal and a decrease in Si-O bond concentrations after the annealing. Variation in binding energies of Si and O with Si concentration (i.e., with depth) has been studied in terms of chemical environments and charging effects. It is found that binding energy of these elements shifts to lower values with increasing Si content. This is a result of less charging due to the presence of easy discharge paths in the Si rich regions of the matrix. Nanocrystal formation leads to even less charging which is probably due to the further increase in conductivity with the formation. (c) 2007 American Institute of Physics.