This paper shows that a structural transition layer of SiO2 exists at an SiO2/Si interface prepared by thermal oxidation of Si. Using a newly developed grazing-incidence x-ray diffraction of synchrotron radiation, the transition layer density (2.4 g/cm(3)) is found to be lower than the immediate bulk SiO2 density (2.6 g/cm(3)), and its thickness is approximately 7 nm. Electrical properties of the SiO2 films are examined by using Fowler-Nordheim tunneling electrons which are injected from the polycrystalline silicon gate electrode into the SiO2 film. The injected charge-to-breakdown (Qbd) rapidly degrades when the SiO2 film thickness decreases below approximately 7 nm due to dielectric breakdown in the transition layer. Based on theoretical analysis, the mechanism of the dielectric breakdown in the transition layer is proposed to be Si-Si bond formations via hypervalent Si atoms and a replacement reaction of an oxygen atom with an electron. Introduction of nitrogen atoms into the transition layer improves the Qbd degradation of thin SiO2 films, because the Si-Si bond formation is suppressed by stress relaxation in the transition layer.