In a method of manufacturing a semiconductor device, a first etching mask and a second etching mask are formed sequentially on a metal gate structure on a substrate and a first insulating interlayer covering a sidewall of the metal gate structure respectively. An opening is formed to expose a top surface of the substrate by removing a portion of the first insulating interlayer not overlapped with the first etching mask or the second etching mask. A metal silicide pattern is formed on the exposed top surface of the substrate. A plug on the metal silicide pattern is formed to fill a remaining portion of the opening. Further, a planarization layer may be used as the second etching mask.