A method for fabricating a vertical channel transistor in a semiconductor device includes forming a plurality of pillars arranged in a first direction and a second direction crossing the first direction over a substrate, wherein each of the pillars includes a hard mask pattern thereon, forming a bit line region in the substrate between the pillars, forming a first sidewall insulation layer on a sidewall of each of the pillars, forming an insulation layer for filling a space between the pillars, forming a mask pattern for exposing the substrate between lines of the pillars arranged in the first direction over a resulting structure including the insulation layer, etching the insulation layer and the substrate using the mask pattern as an etch barrier to form a trench for defining a bit line in the substrate, and forming a second sidewall insulation layer over a resulting structure including the trench.