A method for fabricating a semiconductor device includes forming buried bit lines in a first substrate; forming a trench that separate the buried bit lines from each other; forming an interlayer insulation layer to gap-fill the trench; forming a second substrate over the first substrate gap-filled with the interlayer insulation layer; forming a protective pattern over the second substrate; forming a plurality of active pillars by etching the second substrate using the protective pattern as an etch barrier; and forming vertical gates surrounding sidewalls of the active pillars.