The correlation between the structural and optical properties of Sinanocrystals embedded in SiO2 is the key factor to understandtheir emission mechanism. However, there is a great difficulty in imaging Sinanocrystals in SiO2 and measuring their size distributionbecause of the lack of contrast in electron microscopy. We have used here anew method for imaging Si nanocrystals by using high resolution electronmicroscopy in conjunction with conventional electron microscopy in darkfield conditions. Regarding the optical properties, the band-gap energiesand photoluminescence have been measured by direct and independent methods.The results have allowed experimental determination, for the first time inthis material, of the experimental Stokes shift between absorption andemission as a function of crystallite size. The experimental band-gap versussize correlates well with the most accurate theoretical predictions.Moreover, the photoluminescence energy emission versus crystallite sizeshows a parallel behaviour to that of band-gap energy. Consequently, theexperimental Stokes shift is independent of nanocrystal size and is found tobe 0.26±0.03 eV. This value is almost twice the energy of the Si-O vibration(0.134 eV). These results suggest that the dominant emission of Sinanocrystals passivated with SiO2 is a fundamental transitionspatially located at the Si-SiO2 interface and with theassistance of a local Si-O vibration.