Silicon nanoclusters were formed in plasma-enhanced chemical vapor deposited substoichiometric silicon oxide films by annealing at 1100°C for 1∕2h as a function of different deposition parameters. The samples were analyzed by energy filtered transmission electron microscopy and Rutherford backscattering. At any deposition condition, the clustered silicon concentration is significantly lower than the initial silicon excess concentration. This behavior is explained by taking into account the free energy difference between the metastable SiO and stable SiO2 phase and the strain energy associated with the different atomic densities of Si and SiO2.