According to example embodiments, a method of fabricating a semiconductor device includes alternately stacking interlayer insulating layers and intermediate layers on a substrate, forming openings passing through the interlayer insulating layers and the intermediate layers to form recessed regions in the substrate, forming first epitaxial layers on recessed surfaces in the recessed regions, and forming second epitaxial layers using the first epitaxial layers as seed layers. The second epitaxial layers fill the recessed regions and extend above the substrate.