A three-dimensional semiconductor device is provided including main separation structures disposed on a substrate, and extending in a first direction, parallel to a surface of the substrate; gate electrodes disposed between the main separation structures; a first secondary separation structure penetrating through the gate electrodes, between the main separation structures, and including a first linear portion and a second linear portion, having end portions opposing each other; and second secondary separation structures disposed between the first secondary separation structure and the main separation structures, and penetrating through the gate electrodes. The second secondary separation structures have end portions opposing each other between the second linear portion and the main separation structures.