In a method of manufacturing a semiconductor device, an active channel pattern is formed on a substrate. The active channel pattern includes preliminary gate patterns and single crystalline silicon patterns that are alternately stacked with each other. A source/drain layer is formed on a sidewall of the active channel pattern. Mask pattern structures including a gate trench are formed on the active channel pattern and the source/drain layer. The patterns are selectively etched to form tunnels. The gate trench is then filled with a gate electrode. The gate electrode surrounds the active channel pattern. The gate electrode is protruded from the active channel pattern. The mask pattern structures are then removed. Impurities are implanted into the source/drain regions to form source/drain regions. A silicidation process is carried out on the source/drain regions to form a metal silicide layer, thereby completing a semiconductor device having a MOS transistor.