In a method of manufacturing a semiconductor device to improve structural stability of a semiconductor device in a silicidation process, a substrate is provided to have an active region defined by an isolation layer. An etching mask is formed on the active region and the isolation layer to have a silicidation prevention pattern that at least partially exposes the active region. A gate structure is formed on the exposed active region. A gate spacer is formed on a sidewall of the gate structure positioned on the silicidation prevention pattern. Source/drain regions are formed on the active region using the gate spacer as a mask to thereby form the semiconductor device. Since voids may not be generated in a transistor of the semiconductor device or intrusion of the transistor may be prevented in the silicidation process, the semiconductor device including the transistor may have improved reliability and electrical characteristics.