Disclosed is a method of fabricating a semiconductor device including a multi-gate transistor. The method of fabricating a semiconductor device includes providing a semiconductor device having a number of active patterns which extend in a first direction, are separated by an isolation layer, and covered with a first insulating layer; forming a first groove by etching the isolation layer located between the active patterns adjacent to each other in the first direction; burying the first groove with a passivation layer; forming a second groove exposing at least a portion of both sides of the active patterns by etching the isolation layer located between the active patterns in a second direction intersecting the first direction; removing the passivation layer in the first groove; and forming a gate line filling at least a portion of the second groove and extending in the second direction.