A semiconductor device includes a plurality of first MOS transistors has a first gate electrode formed on a first gate insulating film provided on a semiconductor substrate, a plurality of second MOS transistors has a second gate electrode formed on a second gate insulating film which is provided on the substrate and which is smaller in thickness than the first gate insulating film. A first element isolation region has a first region and a second region, a bottom surface of the second region is deeper than that of the first region by the difference of thickness between the first gate insulating film and the second gate insulating film, and a bottom surface of the first region is equal in a bottom surface of a second element isolation region.