A method of fabricating a semiconductor device, includes (a) forming an oxide film entirely over a silicon substrate on which a MOS transistor is fabricated, (b) carrying out first thermal-annealing to the silicon substrate, (c) removing the oxide film in an area where later mentioned silicide is to be formed, (d) forming a metal film entirely over the silicide substrate, (e) carrying out second thermal-annealing to the silicon substrate to form silicide in the area, and (f) removing the metal film having been not reacted with the silicon substrate.