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High-resolution electron microscopy (HREM) analysis has contributed to the direct analysis of the atomic structures of advanced nanostructured materials, of which properties of these materials are strongly dependent on the atomic arrangements. In the present paper, the direct atomic analysis of nanostructured materials such as borides and oxide materials was described, and the HREM methods were applied to boron nitride nanomaterials such as nanotubes and nanoparticles.