The nucleation and structure of silicon nanocrystals formed by different preparation conditions and silicon concentration (28 -70 area %) have been studied using Transmission Electron Microscopy (TEM), Energy Filtered TEM (EFTEM) and Secondary Ion Mass Spectroscopy (SIMS). The nanocrystals were formed after heat treatment at high temperature of a sputtered 10 nm thick silicon rich oxide on 3 nm SiO2 layer made by Rapid Thermal Oxidation (RTO) of silicon. Nanocrystals precipitate when the excess silicon concentration exceeds 50 area %. Below this percentage amorphous silicon nanoclusters were found. In-situ heat treatment of the samples in the TEM showed that the crystallization requires a temperature above 800 o C. The nanocrystals precipitate in a 4 nm band, 5 nm from the Si substrate and 4 nm from the SiO2 sample surface. The silicon nucleates where the excess Si concentration is the highest. The top surface has less excess Si due to reaction with oxygen from the ambient during annealing. The SiO2-RTO layer is more Si rich due to Si diffusion from the SiO2-Si layer into RTO. Twinning and stacking faults were found in nanocrystals with 4-10 nm in diameter. These types of defects may have large effects upon the usability of the material in electronic devices. Both single and double twin boundaries have been found in the nanocrystals by high resolution transmission electron microscopy (HRTEM). Image simulations were carried out in order to obtain more information about the defects and nanocrystals. The stacking faults are extrinsic and located in the twin boundaries.