An isolation structure of a semiconductor, a semiconductor device having the same, and a method for fabricating the isolation structure are provided. An isolation structure of a semiconductor device may include a trench formed in a substrate, an oxide layer formed on a bottom surface and an inner sidewall of the trench, a filler formed on the oxide layer to fill a part of inside of the trench, and a fourth oxide layer filling an upper portion of the filler of the trench to a height above an upper surface of the trench, an undercut structure being formed on a boundary area between the inner sidewall and the oxide layer.