A method of manufacturing a semiconductor device, which has buried gate electrodes, includes: forming a plurality of gate trenches in a substrate having a plurality of active regions defined by a device isolation film, the plurality of gate trenches crossing the plurality of active regions and extending parallel to each other in a first horizontal direction; selectively forming a first gate insulating layer on an exposed surface of the substrate; forming a second gate insulating layer on exposed surfaces of both the first gate insulating layer and the device isolation film; and forming a plurality of gate insulating layers by partially removing the first gate insulating layer and the second gate insulating layer, and forming a plurality of buried gate electrodes.