We propose a new method for analysis of X-ray emission and Auger electron spectra (XES and AES) of molecules involving the valence spectra using density functional theory (DFT) calculations. To obtain the more accurate transition energies and the relative intensities, we use the total-energy difference procedure (DeltaE-KS) for all transition energies, and transform the coefficients in the LCGTO-MO scheme in the DFT to those for the linear combination of the LCGTO-AO scheme. The method is applied to the analysis of valence spectra, XES and AES for CO and H2O molecules. The simulated spectra are in a good agreement with the experimental results. (C) 20021 Published by Elsevier Science B.V.