Interfaces dramatically affect the properties of materials because their atomic configurations often differ from the bulk material. A determination of the atomic structure of the interface is, therefore, one of the most significant tasks in materials research. Electron microscopy and theoretical calculations have been effectively used to accomplish this important task. In addition, an informatics approach has recently been combined with theoretical calculations to efficiently determine the atomic structures of interfaces. This chapter introduces the determination of interface structures using an informatics approach (Bayesian optimization and virtual screening) along with advanced electron microscopy. In the informatics approach, calculation acceleration on the order of 10 6 can be achieved. Determination of the interface structure with resolution better than ∼45 pm is now possible using advanced electron microscopy. In this way, nanostructures at grain boundaries and heterointerfaces can be qualified. We will introduce these state of the art methods to investigate nanostructures.