Ideally, methods for the characterization of nanostructures would provide intuitively interpretable atomic structure images, along with information on bonding and electronic structure of a particular atomic arrangement. An example in microelectronics where such comprehensive information is necessary are ultrathin layers of alternative high dielectric constant oxides currently investigated to replace SiO₂ as a gate dielectric. This talk will discuss several recent developments in high-spatial resolution analytical methods to characterize the internal atomic and electronic structure, using alternative gate dielectrics as an example. In recent years fundamentally new tools for understanding nanoscale properties have become available through major advances in atomic-level imaging and spectroscopy in scanning transmission electron microscopy (STEM). In STEM, a lattice resolution high-angle annular dark-field, or Z-contrast, image is acquired. The Z-contrast image is chemically sensitive, in particular to heavy elements, and individual atoms can be imaged. In contrast to conventional high-resolution transmission electron microscopy, no preconceived atomic structure models are necessary to interpret the image. The Z-contrast image is also used to position the probe precisely at the region of interest, for example an internal interface or defect, for electron energy-loss spectroscopy (EELS). EELS can be used to profile the chemistry across the films. The near-edge fine-structure of EELS core-loss edges represent the local density of unoccupied states, and can be used to probe bonding changes with near atomic spatial resolution. We discuss limitations of EELS fine-structure analysis, in particular due to the energy-resolution available with current instrumentation and challenges in theoretical methods to calculate EELS fine-structures. However, in both instrumentation and theory, significant progress has been made within the last two years. The talk will also present several complementary methods. In particular, medium energy-ion scattering (MEIS) can provide compositional analysis with sub-nm depth resolution and has a greater sensitivity for heavy elements than EELS. Inelastic electron tunneling spectroscopy (IETS) is a vibrational spectroscopy technique that can provide a wealth of information on bonding, impurities and defects in ultrathin dielectric layers with an excellent energy resolution.