A semiconductor device includes: a semiconductor substrate having first and second areas; an STI isolation region being made of an isolation trench formed in the semiconductor substrate and an insulating film burying the isolation trench and defining a plurality of active regions in the first and second areas; a first structure formed on an area from the active region in the first area to a nearby STI isolation region and having a first height; and a second structure formed on an area from the active region in the second area to a nearby STI isolation region and having a second height, wherein the surface of the said STI isolation region in the first area is lower than the surface of said STI isolation region in the second area.