In methods of fabricating a semiconductor device having multiple channel transistors and semiconductor devices fabricated thereby, the semiconductor device includes an isolation region disposed within a semiconductor substrate and defining a first region. A plurality of semiconductor pillars self-aligned with the first region and spaced apart from each other are disposed within the first region, and each of the semiconductor pillars has at least one recessed region therein. At least one gate structure may be disposed across the recessed regions, which crosses the semiconductor pillars and extends onto the isolation region.