A method of fabricating a semiconductor device includes forming a trench in a semiconductor substrate by a reactive ion etching (RIE) method, the trench having an inner surface, treating the trench with diluted hydrofluoric acid, treating the interior of the trench by a hydrofluoric acid vapor phase cleaning (HFVPC) method, forming a high temperature oxide (HTO) film along the inner surface of the trench, and forming an element isolation insulating film inside the HTO film in the trench so that the trench is filled with the element isolation insulating film.