Disclosed are a light emitting diode and a method of fabricating the same. The light emitting diode includes a GaN substrate having a plurality of through-holes; a GaN-based semiconductor stack structure placed on the substrate and including a first conductive-type semiconductor layer, an active layer, and a second conductive-type semiconductor layer; and a first electrode electrically connected to the first conductive-type semiconductor layer via the through-holes. The light emitting diode can reduce crystal defects and prevent reduction in light emitting area.