The nanopipes in undoped GaN epilayers grown on sapphire substrates were investigated by field emission high-resolution electron microscopy (HREM) and energy-dispersive x-ray spectrometry (EDS). In the HREM images, the cores of the nanopipes appeared disordered in the thin regions and more ordered in the thicker regions, indicating the amorphous layer on the surface has a significant influence on the visible image of the nanopipe in the thin regions. The EDS spectra showed that composition of the materials in nanopipes was mainly oxygen, carbon, and gallium elements. The results suggest that the nanopipes are related to impurities.