A method of making nanometer Si islands for single electron transistors is disclosed. Initially, a pad oxide is deposited over a silicon substrate. Oxygen ions are implanted into the silicon substrate to form an oxygen amorphized region and a high-temperature annealing is performed to form a buried oxide layer in the silicon substrate. Then, a thermal silicon oxide is formed to reduce the thickness of the silicon substrate on the buried oxide layer. The thermal oxide is removed and an ultra-thin oxide layer is then formed on the silicon substrate. A plurality of silicon nitride blocks is formed on the ultra-thin silicon oxide. Afterwards, the spacers of the silicon nitride blocks are formed. The silicon nitride blocks are removed by using wet etching technique. The ultra-thin silicon oxide is etched back and the polysilicon spacers are used as hard mask to Si substrate to form a plurality of nanometer silicon islands. The ultra-thin silicon oxide is removed and an ultra-thin oxynitride layer is regrown on the nanometer silicon islands. Finally, a n+ polysilicon layer is conformally deposited onto the silicon substrate and the nanometer silicon islands.