A semiconductor device including a semiconductor substrate; an element isolation region formed in the substrate including trenches formed at a first depth and being filled with an element isolation insulating film; an element forming region formed on the substrate and being surrounded by the trenches; a gate electrode formed along a first direction on the element forming region via a gate insulating film, the gate electrode extending over the element insulating film filled the trenches extending along a second direction; a source/drain region having a second depth less than the first depth formed in the element forming region beside the gate electrode and having an exposed surface exposed to a trench sidewall; wherein the upper surface of the element isolation insulating film exclusive of a portion underlying the gate electrode is located at a third depth greater than the second depth and less than the first depth.