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The defect structure and morphology of h-GaN film grown by means of MOCVD on (0001) sapphire substrate has been studied by focused ion beam milling (FIB), field emission scanning electron microscopy (FE-SEM), and transmission electron microscopy (TEM). Two different types of grain boundary defects having an anisotropic distribution are observed. For the first type, the grain boundaries surround the pyramid-shaped grains. These defects originate from the mismatch of the crystal lattices between the GaN film and the sapphire substrate. The grain boundary defects penetrate the GaN epilayer and the average grain size increases with increasing layer thickness up to about 500 nm from the interface to the top surface of the GaN film. For the second type, the grain boundaries surround the voids forming produced by impurities in the film. Both types of grain boundaries have a distribution with a hexagonal symmetry that may be the origin of the anisotropic transport properties observed previously in the GaN films.