Analysis of the structures of minerals is an important part of mineralogical investigations. Mineral assemblies are often formed by micro- or even nanocrystals, and it is most interesting to be able to shed light on the crystallography of individual grains, their structure, crystallinity and other properties. This can be done efficiently by the techniques of transmission electron microscopy. Transmission electron microscopy offers not only an ultimate spatial resolution in the imaging mode, but also the possibility of performing diffraction experiments and structure analysis of very small crystals, as well as a range of spectroscopic techniques revealing chemical composition and other properties of the crystals. This chapter reviews the basic techniques of transimssion electron microscopy and their application in mineralogical crystallography. A special emphasis is put on the methods of structure analysis of nanocrystals. This field has seen a rapid evolution in recent years, and has transformed from a being niche technique to a widely accepted and commonly used method of structure analysis. Its applications in mineralogy are especially rich and attractive.