The structures of silicon native oxides formed in the SC-1, H2O2 and wet ozone processes were characterized using X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FT-IR). Spectral simulation was performed to clarify the FT-IR spectra, assuming that the native oxide was pure silicon dioxide. Effective medium theories were applied to understand deviations of the observed spectra from the calculated ones. The deviations between the native oxide thickness evaluated by XPS and the absolute thickness obtained by TEM were also discussed. These deviations can be explained if the void is incorporated in the native oxides and the interface between the native oxide and the basal silicon obtained by the wet ozone process has a relatively smooth surface and a structure more similar to that of pure silicon dioxide, compared with that obtained by SC-1 or H2O2 treatment.