A method of manufacturing a semiconductor device having a doped layer may be provided. The method includes providing a substrate having a first region and a second region, forming a gate dielectric layer on the substrate, forming a first gate electrode layer on the gate dielectric layer, forming a first doped layer on the first gate electrode layer, forming a first capping layer on the first doped layer, forming a mask pattern on the first capping layer in the first region, the mask pattern exposing the first capping layer in the second region, removing the first capping layer and the first doped layer in the second region, removing the mask pattern, and forming a second doped layer on the first capping layer in the first region and the first gate electrode layer in the second region.