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The crystallization of complex oxide thin films on amorphous substrates presents a significant challenge because of the lack of long-range order in these substrates and the subsequent difficulty in controlling crystal growth. Nanocrystals with similar crystal structure have the potential to serve as nucleation sites for crystallization and can facilitate this integration. Isolated nanocrystals of strontium titanate (SrTiO3) can be produced on amorphous SiO2 surfaces through crystallization and ripening of initially amorphous layers of SrTiO3. The resulting SrTiO3 nanocrystals exhibit characteristic lateral radii ranging from tens to hundreds of nm and a consistent average height of 1–2 nm across this range. The area density and mean radii of the nanocrystals can be selected by adjusting the deposition and heating parameters, including the amount of deposited SrTiO3 and the heating duration. The heating-time dependence of the area density and mean radii of the nanocrystals is consistent with predictions based on Ostwald ripening kinetics. The selection of these parameters facilitates the use of SrTiO3 nanocrystals as nucleation sites to crystallize the subsequently deposited layer.