Semiconductor devices and methods of fabricating semiconductor devices that include a substrate and a device isolation layer in the substrate that defines an active region of the substrate are provided. The device isolation layer has a vertically protruding portion having a sidewall that extends vertically beyond a surface of the substrate. An epitaxial layer is provided on the surface of the substrate in the active region and extends onto the device isolation layer. The epitaxial layer is spaced apart from the sidewall of the vertically protruding portion of the device isolation layer. A gate pattern is provided on the epitaxial layer and source/drain regions are provided in the epitaxial layer at opposite sides of the gate pattern.