Example embodiments relate to a method of manufacturing a semiconductor device. Other example embodiments relate to a method of manufacturing a metal-oxide-semiconductor (MOS) transistor having an epitaxial region disposed in a lower portion of sidewalls of a gate pattern. Provided is a method of manufacturing a MOS transistor having an epitaxial region which improves an epitaxial growth rate and which may have fewer defects. The method of manufacturing a MOS transistor having an epitaxial region may include forming a gate pattern on a semiconductor substrate, forming a first ion implantation region having a first damage profile by implanting first impurity ions into the semiconductor substrate using the gate pattern as an ion implantation mask, forming a second ion implantation region having a second damage profile adjacent to the first damage profile by implanting second impurity ions into the semiconductor substrate using the gate pattern as an ion implantation mask and partially etching a lower portion of sidewalls of the gate pattern and forming in-situ an epitaxial region on the etched semiconductor substrate.